CHANGELOG.md
CONTRIBUTING.md
DISCLAIMER.md
LICENSE
MANIFEST.in
README.md
README_CN.md
THIRD_PARTY_NOTICES.md
environment-dev.yml
mkdocs.yml
pyproject.toml
setup.md
setup.py
.github/PULL_REQUEST_TEMPLATE.md
docs/acknowledgements.en.md
docs/acknowledgements.md
docs/agent_tools.en.md
docs/agent_tools.md
docs/changelog.en.md
docs/changelog.md
docs/faq.en.md
docs/faq.md
docs/index.en.md
docs/index.md
docs/installation.en.md
docs/installation.md
docs/api/index.en.md
docs/api/index.md
docs/api/features/01_core_objects.en.md
docs/api/features/01_core_objects.md
docs/api/features/02_io_data.en.md
docs/api/features/02_io_data.md
docs/api/features/03_standardization.en.md
docs/api/features/03_standardization.md
docs/api/features/03_validation.en.md
docs/api/features/03_validation.md
docs/api/features/04_ops_001_sequence_direction.en.md
docs/api/features/04_ops_001_sequence_direction.md
docs/api/features/04_ops_002_transcription_translation.en.md
docs/api/features/04_ops_002_transcription_translation.md
docs/api/features/04_ops_003_subsequence_extraction.en.md
docs/api/features/04_ops_003_subsequence_extraction.md
docs/api/features/04_ops_004_sequence_editing.en.md
docs/api/features/04_ops_004_sequence_editing.md
docs/api/features/04_ops_005_mutation_generation.en.md
docs/api/features/04_ops_005_mutation_generation.md
docs/api/features/04_ops_006_sequence_concatenation.en.md
docs/api/features/04_ops_006_sequence_concatenation.md
docs/api/features/04_ops_008_circular_sequence_operations.en.md
docs/api/features/04_ops_008_circular_sequence_operations.md
docs/api/features/05_all_descriptors.en.md
docs/api/features/05_all_descriptors.md
docs/api/features/06_patterns.en.md
docs/api/features/06_patterns.md
docs/api/features/07_physicochemical.en.md
docs/api/features/07_physicochemical.md
docs/api/features/08_feature_engineering.en.md
docs/api/features/08_feature_engineering.md
docs/api/features/08_fingerprints.en.md
docs/api/features/08_fingerprints.md
docs/api/features/09_alignment.en.md
docs/api/features/09_alignment.md
docs/api/features/09_search.en.md
docs/api/features/09_search.md
docs/api/features/09_similarity_alignment.en.md
docs/api/features/09_similarity_alignment.md
docs/api/features/10_clustering.en.md
docs/api/features/10_clustering.md
docs/api/features/10_datasets.en.md
docs/api/features/10_datasets.md
docs/api/features/10_deduplication.en.md
docs/api/features/10_deduplication.md
docs/api/features/12_evaluation.en.md
docs/api/features/12_evaluation.md
docs/api/features/13_visualization.en.md
docs/api/features/13_visualization.md
docs/api/features/14_engineering.en.md
docs/api/features/14_engineering.md
docs/api/features/15_download.en.md
docs/api/features/15_download.md
docs/api/features/17_sequence_chunking.en.md
docs/api/features/17_sequence_chunking.md
docs/api/features/18_optics_concentration.en.md
docs/api/features/18_optics_concentration.md
docs/api/features/19_duplex_thermodynamics.en.md
docs/api/features/19_duplex_thermodynamics.md
docs/api/features/20_secondary_structure.en.md
docs/api/features/20_secondary_structure.md
docs/api/features/21_structure3d.en.md
docs/api/features/21_structure3d.md
docs/api/features/22_database_query_cancer_variants.en.md
docs/api/features/22_database_query_cancer_variants.md
docs/api/features/22_database_query_clinical_variants.en.md
docs/api/features/22_database_query_clinical_variants.md
docs/api/features/22_database_query_discovery.en.md
docs/api/features/22_database_query_discovery.md
docs/api/features/22_database_query_encode.en.md
docs/api/features/22_database_query_encode.md
docs/api/features/22_database_query_genetic_evidence.en.md
docs/api/features/22_database_query_genetic_evidence.md
docs/api/features/22_database_query_gwas.en.md
docs/api/features/22_database_query_gwas.md
docs/api/features/22_database_query_literature.en.md
docs/api/features/22_database_query_literature.md
docs/api/features/22_database_query_organisms.en.md
docs/api/features/22_database_query_organisms.md
docs/api/features/22_database_query_pathways.en.md
docs/api/features/22_database_query_pathways.md
docs/api/features/22_database_query_phenotypes.en.md
docs/api/features/22_database_query_phenotypes.md
docs/api/features/22_database_query_phewas.en.md
docs/api/features/22_database_query_phewas.md
docs/api/features/22_database_query_population_resources.en.md
docs/api/features/22_database_query_population_resources.md
docs/api/features/22_database_query_regulation.en.md
docs/api/features/22_database_query_regulation.md
docs/api/features/22_database_query_sequences.en.md
docs/api/features/22_database_query_sequences.md
docs/api/features/22_database_query_structural_variants.en.md
docs/api/features/22_database_query_structural_variants.md
docs/api/features/22_database_query_targets.en.md
docs/api/features/22_database_query_targets.md
docs/api/features/22_database_query_variant_frequency.en.md
docs/api/features/22_database_query_variant_frequency.md
docs/api/features/23_prediction_chromatin_classification.en.md
docs/api/features/23_prediction_chromatin_classification.md
docs/api/features/23_prediction_custom_training.en.md
docs/api/features/23_prediction_custom_training.md
docs/api/features/23_prediction_molecular_interactions.en.md
docs/api/features/23_prediction_molecular_interactions.md
docs/api/features/23_prediction_promoter_enhancer.en.md
docs/api/features/23_prediction_promoter_enhancer.md
docs/api/features/23_prediction_protein_features.en.md
docs/api/features/23_prediction_protein_features.md
docs/api/features/23_prediction_regulatory_tracks.en.md
docs/api/features/23_prediction_regulatory_tracks.md
docs/api/features/23_prediction_sequence_classification.en.md
docs/api/features/23_prediction_sequence_classification.md
docs/api/features/23_prediction_splicing_regions.en.md
docs/api/features/23_prediction_splicing_regions.md
docs/api/features/23_prediction_variant_effects.en.md
docs/api/features/23_prediction_variant_effects.md
docs/api/features/26_gene_annotation.en.md
docs/api/features/26_gene_annotation.md
docs/api/features/28_read_processing.en.md
docs/api/features/28_read_processing.md
docs/api/features/29_sequence_optimization.en.md
docs/api/features/29_sequence_optimization.md
docs/api/features/30_phylogeny.en.md
docs/api/features/30_phylogeny.md
docs/api/features/31_statistical_analysis.en.md
docs/api/features/31_statistical_analysis.md
docs/api/features/32_sequencing_analysis.en.md
docs/api/features/32_sequencing_analysis.md
docs/api/features/33_variant_calling.en.md
docs/api/features/33_variant_calling.md
docs/api/features/34_inheritance.en.md
docs/api/features/34_inheritance.md
docs/api/features/35_variant_annotation.en.md
docs/api/features/35_variant_annotation.md
docs/api/features/36_variant_effect_scores.en.md
docs/api/features/36_variant_effect_scores.md
docs/api/features/37_functional_enrichment.en.md
docs/api/features/37_functional_enrichment.md
docs/api/features/38_genomics_extensions.en.md
docs/api/features/38_genomics_extensions.md
docs/api/features/39_external_genomics.en.md
docs/api/features/39_external_genomics.md
docs/api/features/function_tree.en.md
docs/api/features/function_tree.md
docs/assets/data/distribution.csv
docs/demo/data/fixed_demo.json
docs/faq/bioinformatics.en.md
docs/faq/bioinformatics.md
docs/faq/external_analysis_migration.en.md
docs/faq/external_analysis_migration.md
docs/faq/genomics_sources.en.md
docs/faq/genomics_sources.md
docs/faq/tutorial_basics.en.md
docs/faq/tutorial_basics.md
docs/faq/tutorial_integrations.en.md
docs/faq/tutorial_integrations.md
docs/faq/tutorial_overview.en.md
docs/faq/tutorial_overview.md
docs/faq/user_catalog.en.md
docs/faq/user_catalog.md
docs/faq/api/04_ops_001_sequence_direction.en.md
docs/faq/api/04_ops_001_sequence_direction.md
docs/faq/api/04_ops_002_transcription_translation.en.md
docs/faq/api/04_ops_002_transcription_translation.md
docs/faq/api/04_ops_004_sequence_editing.en.md
docs/faq/api/04_ops_004_sequence_editing.md
docs/faq/api/04_ops_006_sequence_concatenation.en.md
docs/faq/api/04_ops_006_sequence_concatenation.md
docs/faq/api/05_all_descriptors.en.md
docs/faq/api/05_all_descriptors.md
docs/faq/api/09_search.en.md
docs/faq/api/09_search.md
docs/faq/api/10_datasets.en.md
docs/faq/api/10_datasets.md
docs/faq/api/14_engineering.en.md
docs/faq/api/14_engineering.md
docs/faq/api/15_download.en.md
docs/faq/api/15_download.md
docs/faq/api/22_database_query_cancer_variants.en.md
docs/faq/api/22_database_query_cancer_variants.md
docs/faq/api/22_database_query_clinical_variants.en.md
docs/faq/api/22_database_query_clinical_variants.md
docs/faq/api/22_database_query_discovery.en.md
docs/faq/api/22_database_query_discovery.md
docs/faq/api/22_database_query_encode.en.md
docs/faq/api/22_database_query_encode.md
docs/faq/api/22_database_query_genetic_evidence.en.md
docs/faq/api/22_database_query_genetic_evidence.md
docs/faq/api/22_database_query_gwas.en.md
docs/faq/api/22_database_query_gwas.md
docs/faq/api/22_database_query_literature.en.md
docs/faq/api/22_database_query_literature.md
docs/faq/api/22_database_query_organisms.en.md
docs/faq/api/22_database_query_organisms.md
docs/faq/api/22_database_query_pathways.en.md
docs/faq/api/22_database_query_pathways.md
docs/faq/api/22_database_query_phenotypes.en.md
docs/faq/api/22_database_query_phenotypes.md
docs/faq/api/22_database_query_phewas.en.md
docs/faq/api/22_database_query_phewas.md
docs/faq/api/22_database_query_population_resources.en.md
docs/faq/api/22_database_query_population_resources.md
docs/faq/api/22_database_query_regulation.en.md
docs/faq/api/22_database_query_regulation.md
docs/faq/api/22_database_query_sequences.en.md
docs/faq/api/22_database_query_sequences.md
docs/faq/api/22_database_query_structural_variants.en.md
docs/faq/api/22_database_query_structural_variants.md
docs/faq/api/22_database_query_targets.en.md
docs/faq/api/22_database_query_targets.md
docs/faq/api/22_database_query_variant_frequency.en.md
docs/faq/api/22_database_query_variant_frequency.md
docs/faq/api/23_prediction_protein_features.en.md
docs/faq/api/23_prediction_protein_features.md
docs/faq/api/23_prediction_regulatory_tracks.en.md
docs/faq/api/23_prediction_regulatory_tracks.md
docs/faq/api/23_prediction_variant_effects.en.md
docs/faq/api/23_prediction_variant_effects.md
docs/faq/api/26_gene_annotation.en.md
docs/faq/api/26_gene_annotation.md
docs/faq/api/30_phylogeny.en.md
docs/faq/api/30_phylogeny.md
docs/faq/api/33_variant_calling.en.md
docs/faq/api/33_variant_calling.md
docs/faq/api/34_inheritance.en.md
docs/faq/api/34_inheritance.md
docs/faq/api/35_variant_annotation.en.md
docs/faq/api/35_variant_annotation.md
docs/faq/api/36_variant_effect_scores.en.md
docs/faq/api/36_variant_effect_scores.md
docs/faq/api/37_functional_enrichment.en.md
docs/faq/api/37_functional_enrichment.md
docs/faq/api/38_genomics_extensions.en.md
docs/faq/api/38_genomics_extensions.md
docs/faq/api/39_external_genomics.en.md
docs/faq/api/39_external_genomics.md
docs/faq/api/index.en.md
docs/faq/api/index.md
docs/llm_tools/agent.en.md
docs/llm_tools/agent.md
docs/llm_tools/mcp.en.md
docs/llm_tools/mcp.md
docs/llm_tools/python_api.en.md
docs/llm_tools/python_api.md
docs/llm_tools/skills.en.md
docs/llm_tools/skills.md
docs/planning/database_capabilities.csv
docs/planning/requirements_traceability.csv
docs/planning/table1_dnakit_capabilities.csv
docs/planning/table1_method_catalog.json
licenses/skills/agentic-science/LICENSE
licenses/skills/biomcp/CITATION.cff
licenses/skills/biomcp/LICENSE
licenses/skills/bionemo/LICENSE
licenses/skills/bionemo/LICENSE-APACHE-2.0
licenses/skills/bionemo/LICENSE-CC-BY-4.0
licenses/skills/bionemo/NOTICE
licenses/skills/bioskills/LICENSE
licenses/skills/clawbio/CITATION.cff
licenses/skills/clawbio/LICENSE
licenses/skills/damlab/LICENSE
licenses/skills/deepmind/LICENSE
licenses/skills/deepmind/README.md
licenses/skills/deepmind/SKILL_LICENSES.md
licenses/skills/encode-toolkit/CITATION.cff
licenses/skills/encode-toolkit/LICENSE
licenses/skills/feynman/LICENSE
licenses/skills/genetic-counseling/LICENSE
licenses/skills/gigwa-mcp/LICENSE
licenses/skills/gigwa-mcp/NOTICE
licenses/skills/haploqtl/CITATION.cff
licenses/skills/haploqtl/LICENSE
licenses/skills/isabl/LICENSE
licenses/skills/kdense/CITATION.cff
licenses/skills/kdense/LICENSE.md
licenses/skills/misha/LICENSE
licenses/skills/misha/LICENSE.md
licenses/skills/myriad/CITATION.cff
licenses/skills/myriad/LICENSE-APACHE-2.0.txt
licenses/skills/myriad/LICENSE-CC-BY-4.0.txt
licenses/skills/myriad/LICENSE.md
licenses/skills/myriad/NOTICE.md
licenses/skills/ngs-tertiary/LICENSE
licenses/skills/omics/LICENSE
licenses/skills/pku-metagenomics/LICENSE
licenses/skills/plant-qpcr/CITATION.cff
licenses/skills/plant-qpcr/LICENSE
licenses/skills/plant-skills/LICENSE
licenses/skills/polyploid-cloning/CITATION.cff
licenses/skills/polyploid-cloning/LICENSE
licenses/skills/research-suite/LICENSE
licenses/skills/research-suite/NOTICE
licenses/skills/sciagent/LICENSE
licenses/skills/statgen-skills/LICENSE
licenses/skills/tangermeme/LICENSE
licenses/skills/tooluniverse/LICENSE
licenses/skills/user335-anthropic/instrument-data-to-allotrope/LICENSE
licenses/skills/user335-anthropic/instrument-data-to-allotrope/LICENSE.txt
licenses/skills/user335-anthropic/instrument-data-to-allotrope/UPSTREAM.md
licenses/skills/user335-anthropic/instrument-data-to-allotrope/references/upstream-readme.md
licenses/skills/user335-anthropic/nextflow-development/LICENSE
licenses/skills/user335-anthropic/nextflow-development/LICENSE.txt
licenses/skills/user335-anthropic/nextflow-development/UPSTREAM.md
licenses/skills/user335-anthropic/nextflow-development/references/upstream-readme.md
licenses/skills/user335-anthropic/scvi-tools/LICENSE
licenses/skills/user335-anthropic/scvi-tools/LICENSE.txt
licenses/skills/user335-anthropic/scvi-tools/UPSTREAM.md
licenses/skills/user335-anthropic/scvi-tools/references/upstream-readme.md
licenses/skills/user335-aws-kiro/kiro-healthomics-genomics/LICENSE
licenses/skills/user335-aws-kiro/kiro-healthomics-genomics/THIRD-PARTY.txt
licenses/skills/user335-aws-kiro/kiro-healthomics-genomics/UPSTREAM.md
licenses/skills/user335-aws-kiro/kiro-healthomics-genomics/references/upstream-readme.md
licenses/skills/user335-bioskills/outlier-splicing-detection/LICENSE
licenses/skills/user335-bioskills/outlier-splicing-detection/UPSTREAM.md
licenses/skills/user335-bioskills/outlier-splicing-detection/references/upstream-readme.md
licenses/skills/user335-bioskills/single-cell-cnv-inference/LICENSE
licenses/skills/user335-bioskills/single-cell-cnv-inference/UPSTREAM.md
licenses/skills/user335-bioskills/single-cell-cnv-inference/references/upstream-readme.md
licenses/skills/user335-clawbio/bioconductor-bridge/LICENSE
licenses/skills/user335-clawbio/bioconductor-bridge/UPSTREAM.md
licenses/skills/user335-clawbio/bioconductor-bridge/references/upstream-readme.md
licenses/skills/user335-clawbio/galaxy-bridge/LICENSE
licenses/skills/user335-clawbio/galaxy-bridge/UPSTREAM.md
licenses/skills/user335-clawbio/galaxy-bridge/references/upstream-readme.md
licenses/skills/user335-clawbio/ukb-ppp-region-fetch/LICENSE
licenses/skills/user335-clawbio/ukb-ppp-region-fetch/UPSTREAM.md
licenses/skills/user335-clawbio/ukb-ppp-region-fetch/bundled_slices/README.md
licenses/skills/user335-clawbio/ukb-ppp-region-fetch/references/upstream-readme.md
licenses/skills/user335-deepmind/interpro-database/LICENSE
licenses/skills/user335-deepmind/interpro-database/SKILL_LICENSES.md
licenses/skills/user335-deepmind/interpro-database/UPSTREAM.md
licenses/skills/user335-deepmind/interpro-database/references/upstream-readme.md
licenses/skills/user335-deepmind/pdb-database/LICENSE
licenses/skills/user335-deepmind/pdb-database/SKILL_LICENSES.md
licenses/skills/user335-deepmind/pdb-database/UPSTREAM.md
licenses/skills/user335-deepmind/pdb-database/references/upstream-readme.md
licenses/skills/user335-galaxy/galaxy-bioblend/LICENSE
licenses/skills/user335-galaxy/galaxy-bioblend/UPSTREAM.md
licenses/skills/user335-galaxy/galaxy-bioblend/references/upstream-readme.md
licenses/skills/user335-kdense/onekgpd-individual-queries/LICENSE
licenses/skills/user335-kdense/onekgpd-individual-queries/UPSTREAM.md
licenses/skills/user335-kdense/onekgpd-individual-queries/references/upstream-readme.md
others/__init__.py
others/examples/README.md
others/examples/advanced_workflow.yml
others/examples/analyze_dna_structures.py
others/examples/bioinformatics_api.py
others/examples/custom_llm.py
others/examples/custom_llm_file.py
others/examples/fixed_demo.fasta
others/examples/fixed_demo_expected.json
others/examples/run_agent_with_memory.py
others/examples/train_custom_properties.py
others/examples/train_machine_learning_properties.py
others/hooks/mcp_setup.py
others/notebooks/00_skeleton_check.ipynb
others/notebooks/01_advanced_workflow.ipynb
others/overrides/main.html
others/overrides/partials/nav.html
others/skills/adaptations.py
others/skills/build_catalog.py
others/skills/build_genomics_survey.py
others/skills/build_native_providers.py
others/skills/build_support_backends.py
others/skills/build_workflow_backends.py
others/skills/curation_rules.py
others/skills/finalize_adaptations.py
others/skills/import_genomics_skills.py
others/skills/import_user_catalog.py
others/skills/import_user_catalog_skills.py
others/skills/normalize_execution_guides.py
others/skills/prepare_all_adaptations.py
others/skills/smoke_workflows.py
others/skills/sync_genomics_expansion.py
others/skills/user_catalog_support.py
others/skills/workflow_corrections.py
others/skills/write_inventory.py
others/skills/write_migration.py
others/skills/adaptations/accessibility-aggregation/DNAKIT.md
others/skills/adaptations/accessibility-aggregation/SKILL.md
others/skills/adaptations/accessibility-aggregation/UPSTREAM.md
others/skills/adaptations/accessibility-aggregation/references/atac-vs-dnase.md
others/skills/adaptations/accessibility-aggregation/references/literature.md
others/skills/adaptations/alignment-amplicon-clipping/DNAKIT.md
others/skills/adaptations/alignment-amplicon-clipping/SKILL.md
others/skills/adaptations/alignment-amplicon-clipping/UPSTREAM.md
others/skills/adaptations/alignment-filtering/DNAKIT.md
others/skills/adaptations/alignment-filtering/SKILL.md
others/skills/adaptations/alignment-filtering/UPSTREAM.md
others/skills/adaptations/alignment-indexing/DNAKIT.md
others/skills/adaptations/alignment-indexing/SKILL.md
others/skills/adaptations/alignment-indexing/UPSTREAM.md
others/skills/adaptations/alignment-io/DNAKIT.md
others/skills/adaptations/alignment-io/SKILL.md
others/skills/adaptations/alignment-io/UPSTREAM.md
others/skills/adaptations/alignment-io/usage-guide.md
others/skills/adaptations/alignment-msa-parsing/DNAKIT.md
others/skills/adaptations/alignment-msa-parsing/SKILL.md
others/skills/adaptations/alignment-msa-parsing/UPSTREAM.md
others/skills/adaptations/alignment-msa-statistics/DNAKIT.md
others/skills/adaptations/alignment-msa-statistics/SKILL.md
others/skills/adaptations/alignment-msa-statistics/UPSTREAM.md
others/skills/adaptations/alignment-multiple/DNAKIT.md
others/skills/adaptations/alignment-multiple/SKILL.md
others/skills/adaptations/alignment-multiple/UPSTREAM.md
others/skills/adaptations/alignment-pairwise/DNAKIT.md
others/skills/adaptations/alignment-pairwise/SKILL.md
others/skills/adaptations/alignment-pairwise/UPSTREAM.md
others/skills/adaptations/alignment-sorting/DNAKIT.md
others/skills/adaptations/alignment-sorting/SKILL.md
others/skills/adaptations/alignment-sorting/UPSTREAM.md
others/skills/adaptations/alignment-trimming/DNAKIT.md
others/skills/adaptations/alignment-trimming/SKILL.md
others/skills/adaptations/alignment-trimming/UPSTREAM.md
others/skills/adaptations/alignment-validation/DNAKIT.md
others/skills/adaptations/alignment-validation/SKILL.md
others/skills/adaptations/alignment-validation/UPSTREAM.md
others/skills/adaptations/alphagem/DNAKIT.md
others/skills/adaptations/alphagem/SKILL.md
others/skills/adaptations/alphagem/UPSTREAM.md
others/skills/adaptations/alphagenome-atlas-website-links/DNAKIT.md
others/skills/adaptations/alphagenome-atlas-website-links/SKILL.md
others/skills/adaptations/alphagenome-atlas-website-links/UPSTREAM.md
others/skills/adaptations/alphagenome-single-variant-analysis/DNAKIT.md
others/skills/adaptations/alphagenome-single-variant-analysis/SKILL.md
others/skills/adaptations/alphagenome-single-variant-analysis/UPSTREAM.md
others/skills/adaptations/alphagenome-variant-impact-score/DNAKIT.md
others/skills/adaptations/alphagenome-variant-impact-score/SKILL.md
others/skills/adaptations/alphagenome-variant-impact-score/UPSTREAM.md
others/skills/adaptations/amplicon-qc/DNAKIT.md
others/skills/adaptations/amplicon-qc/SKILL.md
others/skills/adaptations/amplicon-qc/UPSTREAM.md
others/skills/adaptations/amplicon-qc/amplicon_qc.R
others/skills/adaptations/amplicon-qc/tests/run_test.sh
others/skills/adaptations/analytical-validation/DNAKIT.md
others/skills/adaptations/analytical-validation/SKILL.md
others/skills/adaptations/analytical-validation/UPSTREAM.md
others/skills/adaptations/analyze-fasta/DNAKIT.md
others/skills/adaptations/analyze-fasta/SKILL.md
others/skills/adaptations/analyze-fasta/UPSTREAM.md
others/skills/adaptations/ancestry-risk-profiler/DNAKIT.md
others/skills/adaptations/ancestry-risk-profiler/SKILL.md
others/skills/adaptations/ancestry-risk-profiler/UPSTREAM.md
others/skills/adaptations/ancestry-risk-profiler/ancestry_risk_profiler.py
others/skills/adaptations/ancestry-risk-profiler/tests/test_ancestry_risk_profiler.py
others/skills/adaptations/antismash/DNAKIT.md
others/skills/adaptations/antismash/SKILL.md
others/skills/adaptations/antismash/UPSTREAM.md
others/skills/adaptations/anvio/DNAKIT.md
others/skills/adaptations/anvio/SKILL.md
others/skills/adaptations/anvio/UPSTREAM.md
others/skills/adaptations/article-data-fetcher/DNAKIT.md
others/skills/adaptations/article-data-fetcher/SKILL.md
others/skills/adaptations/article-data-fetcher/UPSTREAM.md
others/skills/adaptations/atac-seq-allele-specific-accessibility/DNAKIT.md
others/skills/adaptations/atac-seq-allele-specific-accessibility/SKILL.md
others/skills/adaptations/atac-seq-allele-specific-accessibility/UPSTREAM.md
others/skills/adaptations/atac-seq-atac-peak-calling/DNAKIT.md
others/skills/adaptations/atac-seq-atac-peak-calling/SKILL.md
others/skills/adaptations/atac-seq-atac-peak-calling/UPSTREAM.md
others/skills/adaptations/atac-seq-atac-qc/DNAKIT.md
others/skills/adaptations/atac-seq-atac-qc/SKILL.md
others/skills/adaptations/atac-seq-atac-qc/UPSTREAM.md
others/skills/adaptations/atac-seq-co-accessibility/DNAKIT.md
others/skills/adaptations/atac-seq-co-accessibility/SKILL.md
others/skills/adaptations/atac-seq-co-accessibility/UPSTREAM.md
others/skills/adaptations/atac-seq-consensus-peakset/DNAKIT.md
others/skills/adaptations/atac-seq-consensus-peakset/SKILL.md
others/skills/adaptations/atac-seq-consensus-peakset/UPSTREAM.md
others/skills/adaptations/atac-seq-deep-learning-atac/DNAKIT.md
others/skills/adaptations/atac-seq-deep-learning-atac/SKILL.md
others/skills/adaptations/atac-seq-deep-learning-atac/UPSTREAM.md
others/skills/adaptations/atac-seq-differential-accessibility/DNAKIT.md
others/skills/adaptations/atac-seq-differential-accessibility/SKILL.md
others/skills/adaptations/atac-seq-differential-accessibility/UPSTREAM.md
others/skills/adaptations/atac-seq-enhancer-gene-linking/DNAKIT.md
others/skills/adaptations/atac-seq-enhancer-gene-linking/SKILL.md
others/skills/adaptations/atac-seq-enhancer-gene-linking/UPSTREAM.md
others/skills/adaptations/atac-seq-footprinting/DNAKIT.md
others/skills/adaptations/atac-seq-footprinting/SKILL.md
others/skills/adaptations/atac-seq-footprinting/UPSTREAM.md
others/skills/adaptations/atac-seq-motif-deviation/DNAKIT.md
others/skills/adaptations/atac-seq-motif-deviation/SKILL.md
others/skills/adaptations/atac-seq-motif-deviation/UPSTREAM.md
others/skills/adaptations/atac-seq-nucleosome-positioning/DNAKIT.md
others/skills/adaptations/atac-seq-nucleosome-positioning/SKILL.md
others/skills/adaptations/atac-seq-nucleosome-positioning/UPSTREAM.md
others/skills/adaptations/atac-seq-single-cell-atac/DNAKIT.md
others/skills/adaptations/atac-seq-single-cell-atac/SKILL.md
others/skills/adaptations/atac-seq-single-cell-atac/UPSTREAM.md
others/skills/adaptations/bam-statistics/DNAKIT.md
others/skills/adaptations/bam-statistics/SKILL.md
others/skills/adaptations/bam-statistics/UPSTREAM.md
others/skills/adaptations/basalt/DNAKIT.md
others/skills/adaptations/basalt/SKILL.md
others/skills/adaptations/basalt/UPSTREAM.md
others/skills/adaptations/batch-analysis/DNAKIT.md
others/skills/adaptations/batch-analysis/SKILL.md
others/skills/adaptations/batch-analysis/UPSTREAM.md
others/skills/adaptations/batch-analysis/references/literature.md
others/skills/adaptations/batch-downloads/DNAKIT.md
others/skills/adaptations/batch-downloads/SKILL.md
others/skills/adaptations/batch-downloads/UPSTREAM.md
others/skills/adaptations/batch-processing/DNAKIT.md
others/skills/adaptations/batch-processing/SKILL.md
others/skills/adaptations/batch-processing/UPSTREAM.md
others/skills/adaptations/benchling-integration/DNAKIT.md
others/skills/adaptations/benchling-integration/SKILL.md
others/skills/adaptations/benchling-integration/UPSTREAM.md
others/skills/adaptations/bigscape/DNAKIT.md
others/skills/adaptations/bigscape/SKILL.md
others/skills/adaptations/bigscape/UPSTREAM.md
others/skills/adaptations/binchicken/DNAKIT.md
others/skills/adaptations/binchicken/SKILL.md
others/skills/adaptations/binchicken/UPSTREAM.md
others/skills/adaptations/binning-qc/DNAKIT.md
others/skills/adaptations/binning-qc/SKILL.md
others/skills/adaptations/binning-qc/UPSTREAM.md
others/skills/adaptations/binning-qc/docs/README.md
others/skills/adaptations/biobakery-databases/DNAKIT.md
others/skills/adaptations/biobakery-databases/SKILL.md
others/skills/adaptations/biobakery-databases/UPSTREAM.md
others/skills/adaptations/bioinfo-pitfalls/DNAKIT.md
others/skills/adaptations/bioinfo-pitfalls/SKILL.md
others/skills/adaptations/bioinfo-pitfalls/UPSTREAM.md
others/skills/adaptations/bioinformatics-methods-results-writer/DNAKIT.md
others/skills/adaptations/bioinformatics-methods-results-writer/SKILL.md
others/skills/adaptations/bioinformatics-methods-results-writer/UPSTREAM.md
others/skills/adaptations/bioinformatics-project/DNAKIT.md
others/skills/adaptations/bioinformatics-project/SKILL.md
others/skills/adaptations/bioinformatics-project/UPSTREAM.md
others/skills/adaptations/biomart-queries/DNAKIT.md
others/skills/adaptations/biomart-queries/SKILL.md
others/skills/adaptations/biomart-queries/UPSTREAM.md
others/skills/adaptations/bioservices-multi-database/DNAKIT.md
others/skills/adaptations/bioservices-multi-database/SKILL.md
others/skills/adaptations/bioservices-multi-database/UPSTREAM.md
others/skills/adaptations/biosurfdb/DNAKIT.md
others/skills/adaptations/biosurfdb/SKILL.md
others/skills/adaptations/biosurfdb/UPSTREAM.md
others/skills/adaptations/blast-searches/DNAKIT.md
others/skills/adaptations/blast-searches/SKILL.md
others/skills/adaptations/blast-searches/UPSTREAM.md
others/skills/adaptations/borzoi/DNAKIT.md
others/skills/adaptations/borzoi/SKILL.md
others/skills/adaptations/borzoi/UPSTREAM.md
others/skills/adaptations/busco-assessor/DNAKIT.md
others/skills/adaptations/busco-assessor/SKILL.md
others/skills/adaptations/busco-assessor/UPSTREAM.md
others/skills/adaptations/busco-assessor/busco_assessor.py
others/skills/adaptations/busco-status-interpretation/DNAKIT.md
others/skills/adaptations/busco-status-interpretation/SKILL.md
others/skills/adaptations/busco-status-interpretation/UPSTREAM.md
others/skills/adaptations/caduceus/DNAKIT.md
others/skills/adaptations/caduceus/SKILL.md
others/skills/adaptations/caduceus/UPSTREAM.md
others/skills/adaptations/cami/DNAKIT.md
others/skills/adaptations/cami/SKILL.md
others/skills/adaptations/cami/UPSTREAM.md
others/skills/adaptations/cancer-genomics-tcga/DNAKIT.md
others/skills/adaptations/cancer-genomics-tcga/SKILL.md
others/skills/adaptations/cancer-genomics-tcga/UPSTREAM.md
others/skills/adaptations/cancer-variant-interpretation/ANALYSIS_DETAILS.md
others/skills/adaptations/cancer-variant-interpretation/DNAKIT.md
others/skills/adaptations/cancer-variant-interpretation/EXAMPLES.md
others/skills/adaptations/cancer-variant-interpretation/QUICK_START.md
others/skills/adaptations/cancer-variant-interpretation/SKILL.md
others/skills/adaptations/cancer-variant-interpretation/TOOLS_REFERENCE.md
others/skills/adaptations/cancer-variant-interpretation/UPSTREAM.md
others/skills/adaptations/cancer-variant-interpretation/test_skill.py
others/skills/adaptations/causal-genomics-colocalization-analysis/DNAKIT.md
others/skills/adaptations/causal-genomics-colocalization-analysis/SKILL.md
others/skills/adaptations/causal-genomics-colocalization-analysis/UPSTREAM.md
others/skills/adaptations/causal-genomics-effector-gene-prioritization/DNAKIT.md
others/skills/adaptations/causal-genomics-effector-gene-prioritization/SKILL.md
others/skills/adaptations/causal-genomics-effector-gene-prioritization/UPSTREAM.md
others/skills/adaptations/causal-genomics-fine-mapping/DNAKIT.md
others/skills/adaptations/causal-genomics-fine-mapping/SKILL.md
others/skills/adaptations/causal-genomics-fine-mapping/UPSTREAM.md
others/skills/adaptations/causal-genomics-genetic-correlation/DNAKIT.md
others/skills/adaptations/causal-genomics-genetic-correlation/SKILL.md
others/skills/adaptations/causal-genomics-genetic-correlation/UPSTREAM.md
others/skills/adaptations/causal-genomics-genomic-sem/DNAKIT.md
others/skills/adaptations/causal-genomics-genomic-sem/SKILL.md
others/skills/adaptations/causal-genomics-genomic-sem/UPSTREAM.md
others/skills/adaptations/causal-genomics-heritability-partitioning/DNAKIT.md
others/skills/adaptations/causal-genomics-heritability-partitioning/SKILL.md
others/skills/adaptations/causal-genomics-heritability-partitioning/UPSTREAM.md
others/skills/adaptations/causal-genomics-mediation-analysis/DNAKIT.md
others/skills/adaptations/causal-genomics-mediation-analysis/SKILL.md
others/skills/adaptations/causal-genomics-mediation-analysis/UPSTREAM.md
others/skills/adaptations/causal-genomics-mendelian-randomization/DNAKIT.md
others/skills/adaptations/causal-genomics-mendelian-randomization/SKILL.md
others/skills/adaptations/causal-genomics-mendelian-randomization/UPSTREAM.md
others/skills/adaptations/causal-genomics-pleiotropy-detection/DNAKIT.md
others/skills/adaptations/causal-genomics-pleiotropy-detection/SKILL.md
others/skills/adaptations/causal-genomics-pleiotropy-detection/UPSTREAM.md
others/skills/adaptations/causal-genomics-proteome-mr-drug-target/DNAKIT.md
others/skills/adaptations/causal-genomics-proteome-mr-drug-target/SKILL.md
others/skills/adaptations/causal-genomics-proteome-mr-drug-target/UPSTREAM.md
others/skills/adaptations/causal-genomics-transcriptome-wide-association/DNAKIT.md
others/skills/adaptations/causal-genomics-transcriptome-wide-association/SKILL.md
others/skills/adaptations/causal-genomics-transcriptome-wide-association/UPSTREAM.md
others/skills/adaptations/cbioportal-database/DNAKIT.md
others/skills/adaptations/cbioportal-database/SKILL.md
others/skills/adaptations/cbioportal-database/UPSTREAM.md
others/skills/adaptations/cfdna-preprocessing/DNAKIT.md
others/skills/adaptations/cfdna-preprocessing/SKILL.md
others/skills/adaptations/cfdna-preprocessing/UPSTREAM.md
others/skills/adaptations/checkm2/DNAKIT.md
others/skills/adaptations/checkm2/SKILL.md
others/skills/adaptations/checkm2/UPSTREAM.md
others/skills/adaptations/checkv/DNAKIT.md
others/skills/adaptations/checkv/SKILL.md
others/skills/adaptations/checkv/UPSTREAM.md
others/skills/adaptations/chip-atlas-diff-analysis/DNAKIT.md
others/skills/adaptations/chip-atlas-diff-analysis/SKILL.md
others/skills/adaptations/chip-atlas-diff-analysis/UPSTREAM.md
others/skills/adaptations/chip-atlas-peak-enrichment/DNAKIT.md
others/skills/adaptations/chip-atlas-peak-enrichment/SKILL.md
others/skills/adaptations/chip-atlas-peak-enrichment/UPSTREAM.md
others/skills/adaptations/chip-atlas-target-genes/DNAKIT.md
others/skills/adaptations/chip-atlas-target-genes/SKILL.md
others/skills/adaptations/chip-atlas-target-genes/UPSTREAM.md
others/skills/adaptations/chipseq-allele-specific-binding/DNAKIT.md
others/skills/adaptations/chipseq-allele-specific-binding/SKILL.md
others/skills/adaptations/chipseq-allele-specific-binding/UPSTREAM.md
others/skills/adaptations/chipseq-chip-deep-learning/DNAKIT.md
others/skills/adaptations/chipseq-chip-deep-learning/SKILL.md
others/skills/adaptations/chipseq-chip-deep-learning/UPSTREAM.md
others/skills/adaptations/chipseq-chromatin-state-segmentation/DNAKIT.md
others/skills/adaptations/chipseq-chromatin-state-segmentation/SKILL.md
others/skills/adaptations/chipseq-chromatin-state-segmentation/UPSTREAM.md
others/skills/adaptations/chipseq-cut-and-run-tag/DNAKIT.md
others/skills/adaptations/chipseq-cut-and-run-tag/SKILL.md
others/skills/adaptations/chipseq-cut-and-run-tag/UPSTREAM.md
others/skills/adaptations/chipseq-differential-binding/DNAKIT.md
others/skills/adaptations/chipseq-differential-binding/SKILL.md
others/skills/adaptations/chipseq-differential-binding/UPSTREAM.md
others/skills/adaptations/chipseq-motif-analysis/DNAKIT.md
others/skills/adaptations/chipseq-motif-analysis/SKILL.md
others/skills/adaptations/chipseq-motif-analysis/UPSTREAM.md
others/skills/adaptations/chipseq-peak-annotation/DNAKIT.md
others/skills/adaptations/chipseq-peak-annotation/SKILL.md
others/skills/adaptations/chipseq-peak-annotation/UPSTREAM.md
others/skills/adaptations/chipseq-peak-calling/DNAKIT.md
others/skills/adaptations/chipseq-peak-calling/SKILL.md
others/skills/adaptations/chipseq-peak-calling/UPSTREAM.md
others/skills/adaptations/chipseq-qc/DNAKIT.md
others/skills/adaptations/chipseq-qc/SKILL.md
others/skills/adaptations/chipseq-qc/UPSTREAM.md
others/skills/adaptations/chipseq-spike-in-normalization/DNAKIT.md
others/skills/adaptations/chipseq-spike-in-normalization/SKILL.md
others/skills/adaptations/chipseq-spike-in-normalization/UPSTREAM.md
others/skills/adaptations/chipseq-super-enhancers/DNAKIT.md
others/skills/adaptations/chipseq-super-enhancers/SKILL.md
others/skills/adaptations/chipseq-super-enhancers/UPSTREAM.md
others/skills/adaptations/chipseq-visualization/DNAKIT.md
others/skills/adaptations/chipseq-visualization/SKILL.md
others/skills/adaptations/chipseq-visualization/UPSTREAM.md
others/skills/adaptations/cite-encode/DNAKIT.md
others/skills/adaptations/cite-encode/SKILL.md
others/skills/adaptations/cite-encode/UPSTREAM.md
others/skills/adaptations/cite-encode/references/literature.md
others/skills/adaptations/clinical-databases-acmg-classification/DNAKIT.md
others/skills/adaptations/clinical-databases-acmg-classification/SKILL.md
others/skills/adaptations/clinical-databases-acmg-classification/UPSTREAM.md
others/skills/adaptations/clinical-databases-clinvar-lookup/DNAKIT.md
others/skills/adaptations/clinical-databases-clinvar-lookup/SKILL.md
others/skills/adaptations/clinical-databases-clinvar-lookup/UPSTREAM.md
others/skills/adaptations/clinical-databases-dbsnp-queries/DNAKIT.md
others/skills/adaptations/clinical-databases-dbsnp-queries/SKILL.md
others/skills/adaptations/clinical-databases-dbsnp-queries/UPSTREAM.md
others/skills/adaptations/clinical-databases-gnomad-frequencies/DNAKIT.md
others/skills/adaptations/clinical-databases-gnomad-frequencies/SKILL.md
others/skills/adaptations/clinical-databases-gnomad-frequencies/UPSTREAM.md
others/skills/adaptations/clinical-databases-hla-typing/DNAKIT.md
others/skills/adaptations/clinical-databases-hla-typing/SKILL.md
others/skills/adaptations/clinical-databases-hla-typing/UPSTREAM.md
others/skills/adaptations/clinical-databases-msi-detection/DNAKIT.md
others/skills/adaptations/clinical-databases-msi-detection/SKILL.md
others/skills/adaptations/clinical-databases-msi-detection/UPSTREAM.md
others/skills/adaptations/clinical-databases-myvariant-queries/DNAKIT.md
others/skills/adaptations/clinical-databases-myvariant-queries/SKILL.md
others/skills/adaptations/clinical-databases-myvariant-queries/UPSTREAM.md
others/skills/adaptations/clinical-databases-pharmacogenomics/DNAKIT.md
others/skills/adaptations/clinical-databases-pharmacogenomics/SKILL.md
others/skills/adaptations/clinical-databases-pharmacogenomics/UPSTREAM.md
others/skills/adaptations/clinical-databases-polygenic-risk/DNAKIT.md
others/skills/adaptations/clinical-databases-polygenic-risk/SKILL.md
others/skills/adaptations/clinical-databases-polygenic-risk/UPSTREAM.md
others/skills/adaptations/clinical-databases-somatic-signatures/DNAKIT.md
others/skills/adaptations/clinical-databases-somatic-signatures/SKILL.md
others/skills/adaptations/clinical-databases-somatic-signatures/UPSTREAM.md
others/skills/adaptations/clinical-databases-tumor-mutational-burden/DNAKIT.md
others/skills/adaptations/clinical-databases-tumor-mutational-burden/SKILL.md
others/skills/adaptations/clinical-databases-tumor-mutational-burden/UPSTREAM.md
others/skills/adaptations/clinical-databases-variant-prioritization/DNAKIT.md
others/skills/adaptations/clinical-databases-variant-prioritization/SKILL.md
others/skills/adaptations/clinical-databases-variant-prioritization/UPSTREAM.md
others/skills/adaptations/clinpgx/DNAKIT.md
others/skills/adaptations/clinpgx/SKILL.md
others/skills/adaptations/clinpgx/UPSTREAM.md
others/skills/adaptations/clinpgx/api.py
others/skills/adaptations/clinpgx/clinpgx.py
others/skills/adaptations/codon-usage/DNAKIT.md
others/skills/adaptations/codon-usage/SKILL.md
others/skills/adaptations/codon-usage/UPSTREAM.md
others/skills/adaptations/comparative-genomics/DNAKIT.md
others/skills/adaptations/comparative-genomics/SKILL.md
others/skills/adaptations/comparative-genomics/UPSTREAM.md
others/skills/adaptations/comparative-genomics-ancestral-reconstruction/DNAKIT.md
others/skills/adaptations/comparative-genomics-ancestral-reconstruction/SKILL.md
others/skills/adaptations/comparative-genomics-ancestral-reconstruction/UPSTREAM.md
others/skills/adaptations/comparative-genomics-comparative-annotation-projection/DNAKIT.md
others/skills/adaptations/comparative-genomics-comparative-annotation-projection/SKILL.md
others/skills/adaptations/comparative-genomics-comparative-annotation-projection/UPSTREAM.md
others/skills/adaptations/comparative-genomics-gene-family-evolution/DNAKIT.md
others/skills/adaptations/comparative-genomics-gene-family-evolution/SKILL.md
others/skills/adaptations/comparative-genomics-gene-family-evolution/UPSTREAM.md
others/skills/adaptations/comparative-genomics-gene-tree-species-tree-reconciliation/DNAKIT.md
others/skills/adaptations/comparative-genomics-gene-tree-species-tree-reconciliation/SKILL.md
others/skills/adaptations/comparative-genomics-gene-tree-species-tree-reconciliation/UPSTREAM.md
others/skills/adaptations/comparative-genomics-genome-distance-and-species-delineation/DNAKIT.md
others/skills/adaptations/comparative-genomics-genome-distance-and-species-delineation/SKILL.md
others/skills/adaptations/comparative-genomics-genome-distance-and-species-delineation/UPSTREAM.md
others/skills/adaptations/comparative-genomics-hgt-detection/DNAKIT.md
others/skills/adaptations/comparative-genomics-hgt-detection/SKILL.md
others/skills/adaptations/comparative-genomics-hgt-detection/UPSTREAM.md
others/skills/adaptations/comparative-genomics-introgression-detection/DNAKIT.md
others/skills/adaptations/comparative-genomics-introgression-detection/SKILL.md
others/skills/adaptations/comparative-genomics-introgression-detection/UPSTREAM.md
others/skills/adaptations/comparative-genomics-ortholog-inference/DNAKIT.md
others/skills/adaptations/comparative-genomics-ortholog-inference/SKILL.md
others/skills/adaptations/comparative-genomics-ortholog-inference/UPSTREAM.md
others/skills/adaptations/comparative-genomics-pangenome-analysis/DNAKIT.md
others/skills/adaptations/comparative-genomics-pangenome-analysis/SKILL.md
others/skills/adaptations/comparative-genomics-pangenome-analysis/UPSTREAM.md
others/skills/adaptations/comparative-genomics-positive-selection/DNAKIT.md
others/skills/adaptations/comparative-genomics-positive-selection/SKILL.md
others/skills/adaptations/comparative-genomics-positive-selection/UPSTREAM.md
others/skills/adaptations/comparative-genomics-synteny-analysis/DNAKIT.md
others/skills/adaptations/comparative-genomics-synteny-analysis/SKILL.md
others/skills/adaptations/comparative-genomics-synteny-analysis/UPSTREAM.md
others/skills/adaptations/comparative-genomics-whole-genome-alignment/DNAKIT.md
others/skills/adaptations/comparative-genomics-whole-genome-alignment/SKILL.md
others/skills/adaptations/comparative-genomics-whole-genome-alignment/UPSTREAM.md
others/skills/adaptations/comparative-genomics-whole-genome-duplication/DNAKIT.md
others/skills/adaptations/comparative-genomics-whole-genome-duplication/SKILL.md
others/skills/adaptations/comparative-genomics-whole-genome-duplication/UPSTREAM.md
others/skills/adaptations/compare-biosamples/DNAKIT.md
others/skills/adaptations/compare-biosamples/SKILL.md
others/skills/adaptations/compare-biosamples/UPSTREAM.md
others/skills/adaptations/compare-biosamples/references/literature.md
others/skills/adaptations/compressed-files/DNAKIT.md
others/skills/adaptations/compressed-files/SKILL.md
others/skills/adaptations/compressed-files/UPSTREAM.md
others/skills/adaptations/consensus-sequences/DNAKIT.md
others/skills/adaptations/consensus-sequences/SKILL.md
others/skills/adaptations/consensus-sequences/UPSTREAM.md
others/skills/adaptations/copy-number-allele-specific-copy-number/DNAKIT.md
others/skills/adaptations/copy-number-allele-specific-copy-number/SKILL.md
others/skills/adaptations/copy-number-allele-specific-copy-number/UPSTREAM.md
others/skills/adaptations/copy-number-cnv-annotation/DNAKIT.md
others/skills/adaptations/copy-number-cnv-annotation/SKILL.md
others/skills/adaptations/copy-number-cnv-annotation/UPSTREAM.md
others/skills/adaptations/copy-number-cnv-visualization/DNAKIT.md
others/skills/adaptations/copy-number-cnv-visualization/SKILL.md
others/skills/adaptations/copy-number-cnv-visualization/UPSTREAM.md
others/skills/adaptations/copy-number-cnvkit-analysis/DNAKIT.md
others/skills/adaptations/copy-number-cnvkit-analysis/SKILL.md
others/skills/adaptations/copy-number-cnvkit-analysis/UPSTREAM.md
others/skills/adaptations/copy-number-copy-ratio-segmentation/DNAKIT.md
others/skills/adaptations/copy-number-copy-ratio-segmentation/SKILL.md
others/skills/adaptations/copy-number-copy-ratio-segmentation/UPSTREAM.md
others/skills/adaptations/copy-number-focal-amplification-ecdna/DNAKIT.md
others/skills/adaptations/copy-number-focal-amplification-ecdna/SKILL.md
others/skills/adaptations/copy-number-focal-amplification-ecdna/UPSTREAM.md
others/skills/adaptations/copy-number-gatk-cnv/DNAKIT.md
others/skills/adaptations/copy-number-gatk-cnv/SKILL.md
others/skills/adaptations/copy-number-gatk-cnv/UPSTREAM.md
others/skills/adaptations/copy-number-germline-cnv-interpretation/DNAKIT.md
others/skills/adaptations/copy-number-germline-cnv-interpretation/SKILL.md
others/skills/adaptations/copy-number-germline-cnv-interpretation/UPSTREAM.md
others/skills/adaptations/copy-number-hrd-scoring/DNAKIT.md
others/skills/adaptations/copy-number-hrd-scoring/SKILL.md
others/skills/adaptations/copy-number-hrd-scoring/UPSTREAM.md
others/skills/adaptations/copy-number-recurrent-cnv/DNAKIT.md
others/skills/adaptations/copy-number-recurrent-cnv/SKILL.md
others/skills/adaptations/copy-number-recurrent-cnv/UPSTREAM.md
others/skills/adaptations/copy-number-subclonal-copy-number/DNAKIT.md
others/skills/adaptations/copy-number-subclonal-copy-number/SKILL.md
others/skills/adaptations/copy-number-subclonal-copy-number/UPSTREAM.md
others/skills/adaptations/cosmic-database/DNAKIT.md
others/skills/adaptations/cosmic-database/SKILL.md
others/skills/adaptations/cosmic-database/UPSTREAM.md
others/skills/adaptations/crispr-screen-triage/DNAKIT.md
others/skills/adaptations/crispr-screen-triage/SKILL.md
others/skills/adaptations/crispr-screen-triage/UPSTREAM.md
others/skills/adaptations/crispr-screens-bagel-essentiality/DNAKIT.md
others/skills/adaptations/crispr-screens-bagel-essentiality/SKILL.md
others/skills/adaptations/crispr-screens-bagel-essentiality/UPSTREAM.md
others/skills/adaptations/crispr-screens-base-editing-analysis/DNAKIT.md
others/skills/adaptations/crispr-screens-base-editing-analysis/SKILL.md
others/skills/adaptations/crispr-screens-base-editing-analysis/UPSTREAM.md
others/skills/adaptations/crispr-screens-batch-correction/DNAKIT.md
others/skills/adaptations/crispr-screens-batch-correction/SKILL.md
others/skills/adaptations/crispr-screens-batch-correction/UPSTREAM.md
others/skills/adaptations/crispr-screens-combinatorial-screens/DNAKIT.md
others/skills/adaptations/crispr-screens-combinatorial-screens/SKILL.md
others/skills/adaptations/crispr-screens-combinatorial-screens/UPSTREAM.md
others/skills/adaptations/crispr-screens-copy-number-correction/DNAKIT.md
others/skills/adaptations/crispr-screens-copy-number-correction/SKILL.md
others/skills/adaptations/crispr-screens-copy-number-correction/UPSTREAM.md
others/skills/adaptations/crispr-screens-crispresso-editing/DNAKIT.md
others/skills/adaptations/crispr-screens-crispresso-editing/SKILL.md
others/skills/adaptations/crispr-screens-crispresso-editing/UPSTREAM.md
others/skills/adaptations/crispr-screens-drugz-chemogenomic/DNAKIT.md
others/skills/adaptations/crispr-screens-drugz-chemogenomic/SKILL.md
others/skills/adaptations/crispr-screens-drugz-chemogenomic/UPSTREAM.md
others/skills/adaptations/crispr-screens-hit-calling/DNAKIT.md
others/skills/adaptations/crispr-screens-hit-calling/SKILL.md
others/skills/adaptations/crispr-screens-hit-calling/UPSTREAM.md
others/skills/adaptations/crispr-screens-in-vivo-screens/DNAKIT.md
others/skills/adaptations/crispr-screens-in-vivo-screens/SKILL.md
others/skills/adaptations/crispr-screens-in-vivo-screens/UPSTREAM.md
others/skills/adaptations/crispr-screens-jacks-analysis/DNAKIT.md
others/skills/adaptations/crispr-screens-jacks-analysis/SKILL.md
others/skills/adaptations/crispr-screens-jacks-analysis/UPSTREAM.md
others/skills/adaptations/crispr-screens-library-design/DNAKIT.md
others/skills/adaptations/crispr-screens-library-design/SKILL.md
others/skills/adaptations/crispr-screens-library-design/UPSTREAM.md
others/skills/adaptations/crispr-screens-mageck-analysis/DNAKIT.md
others/skills/adaptations/crispr-screens-mageck-analysis/SKILL.md
others/skills/adaptations/crispr-screens-mageck-analysis/UPSTREAM.md
others/skills/adaptations/crispr-screens-perturb-seq-analysis/DNAKIT.md
others/skills/adaptations/crispr-screens-perturb-seq-analysis/SKILL.md
others/skills/adaptations/crispr-screens-perturb-seq-analysis/UPSTREAM.md
others/skills/adaptations/crispr-screens-prime-editing-screens/DNAKIT.md
others/skills/adaptations/crispr-screens-prime-editing-screens/SKILL.md
others/skills/adaptations/crispr-screens-prime-editing-screens/UPSTREAM.md
others/skills/adaptations/crispr-screens-screen-qc/DNAKIT.md
others/skills/adaptations/crispr-screens-screen-qc/SKILL.md
others/skills/adaptations/crispr-screens-screen-qc/UPSTREAM.md
others/skills/adaptations/ctdna-mutation-detection/DNAKIT.md
others/skills/adaptations/ctdna-mutation-detection/SKILL.md
others/skills/adaptations/ctdna-mutation-detection/UPSTREAM.md
others/skills/adaptations/data-provenance/DNAKIT.md
others/skills/adaptations/data-provenance/SKILL.md
others/skills/adaptations/data-provenance/UPSTREAM.md
others/skills/adaptations/data-provenance/references/literature.md
others/skills/adaptations/data-visualization-circos-plots/DNAKIT.md
others/skills/adaptations/data-visualization-circos-plots/SKILL.md
others/skills/adaptations/data-visualization-circos-plots/UPSTREAM.md
others/skills/adaptations/data-visualization-genome-tracks/DNAKIT.md
others/skills/adaptations/data-visualization-genome-tracks/SKILL.md
others/skills/adaptations/data-visualization-genome-tracks/UPSTREAM.md
others/skills/adaptations/data-visualization-lollipop-protein-maps/DNAKIT.md
others/skills/adaptations/data-visualization-lollipop-protein-maps/SKILL.md
others/skills/adaptations/data-visualization-lollipop-protein-maps/UPSTREAM.md
others/skills/adaptations/data-visualization-manhattan-qq-locuszoom/DNAKIT.md
others/skills/adaptations/data-visualization-manhattan-qq-locuszoom/SKILL.md
others/skills/adaptations/data-visualization-manhattan-qq-locuszoom/UPSTREAM.md
others/skills/adaptations/data-visualization-oncoprint-mutation-matrices/DNAKIT.md
others/skills/adaptations/data-visualization-oncoprint-mutation-matrices/SKILL.md
others/skills/adaptations/data-visualization-oncoprint-mutation-matrices/UPSTREAM.md
others/skills/adaptations/data-visualization-sequence-logos/DNAKIT.md
others/skills/adaptations/data-visualization-sequence-logos/SKILL.md
others/skills/adaptations/data-visualization-sequence-logos/UPSTREAM.md
others/skills/adaptations/dbcan/DNAKIT.md
others/skills/adaptations/dbcan/SKILL.md
others/skills/adaptations/dbcan/UPSTREAM.md
others/skills/adaptations/deeptools-ngs-analysis/DNAKIT.md
others/skills/adaptations/deeptools-ngs-analysis/SKILL.md
others/skills/adaptations/deeptools-ngs-analysis/UPSTREAM.md
others/skills/adaptations/deepurify/DNAKIT.md
others/skills/adaptations/deepurify/SKILL.md
others/skills/adaptations/deepurify/UPSTREAM.md
others/skills/adaptations/defensefinder/DNAKIT.md
others/skills/adaptations/defensefinder/SKILL.md
others/skills/adaptations/defensefinder/UPSTREAM.md
others/skills/adaptations/depmap-crispr-essentiality/DNAKIT.md
others/skills/adaptations/depmap-crispr-essentiality/SKILL.md
others/skills/adaptations/depmap-crispr-essentiality/UPSTREAM.md
others/skills/adaptations/disinfinder/DNAKIT.md
others/skills/adaptations/disinfinder/SKILL.md
others/skills/adaptations/disinfinder/UPSTREAM.md
others/skills/adaptations/dnabert2/DNAKIT.md
others/skills/adaptations/dnabert2/SKILL.md
others/skills/adaptations/dnabert2/UPSTREAM.md
others/skills/adaptations/dnakit/DNAKIT.md
others/skills/adaptations/dnakit/SKILL.md
others/skills/adaptations/dnakit/UPSTREAM.md
others/skills/adaptations/dnanexus-integration/DNAKIT.md
others/skills/adaptations/dnanexus-integration/SKILL.md
others/skills/adaptations/dnanexus-integration/UPSTREAM.md
others/skills/adaptations/dom-biosurfactant/DNAKIT.md
others/skills/adaptations/dom-biosurfactant/SKILL.md
others/skills/adaptations/dom-biosurfactant/UPSTREAM.md
others/skills/adaptations/draft-counseling-summary/DNAKIT.md
others/skills/adaptations/draft-counseling-summary/SKILL.md
others/skills/adaptations/draft-counseling-summary/UPSTREAM.md
others/skills/adaptations/dram/DNAKIT.md
others/skills/adaptations/dram/SKILL.md
others/skills/adaptations/dram/UPSTREAM.md
others/skills/adaptations/draw-pedigree/DNAKIT.md
others/skills/adaptations/draw-pedigree/SKILL.md
others/skills/adaptations/draw-pedigree/UPSTREAM.md
others/skills/adaptations/duplicate-handling/DNAKIT.md
others/skills/adaptations/duplicate-handling/SKILL.md
others/skills/adaptations/duplicate-handling/UPSTREAM.md
others/skills/adaptations/ecological-genomics-biodiversity-metrics/DNAKIT.md
others/skills/adaptations/ecological-genomics-biodiversity-metrics/SKILL.md
others/skills/adaptations/ecological-genomics-biodiversity-metrics/UPSTREAM.md
others/skills/adaptations/ecological-genomics-community-ecology/DNAKIT.md
others/skills/adaptations/ecological-genomics-community-ecology/SKILL.md
others/skills/adaptations/ecological-genomics-community-ecology/UPSTREAM.md
others/skills/adaptations/ecological-genomics-conservation-genetics/DNAKIT.md
others/skills/adaptations/ecological-genomics-conservation-genetics/SKILL.md
others/skills/adaptations/ecological-genomics-conservation-genetics/UPSTREAM.md
others/skills/adaptations/ecological-genomics-edna-metabarcoding/DNAKIT.md
others/skills/adaptations/ecological-genomics-edna-metabarcoding/SKILL.md
others/skills/adaptations/ecological-genomics-edna-metabarcoding/UPSTREAM.md
others/skills/adaptations/ecological-genomics-landscape-genomics/DNAKIT.md
others/skills/adaptations/ecological-genomics-landscape-genomics/SKILL.md
others/skills/adaptations/ecological-genomics-landscape-genomics/UPSTREAM.md
others/skills/adaptations/ecological-genomics-species-delimitation/DNAKIT.md
others/skills/adaptations/ecological-genomics-species-delimitation/SKILL.md
others/skills/adaptations/ecological-genomics-species-delimitation/UPSTREAM.md
others/skills/adaptations/element-cycling/DNAKIT.md
others/skills/adaptations/element-cycling/SKILL.md
others/skills/adaptations/element-cycling/UPSTREAM.md
others/skills/adaptations/ena-database/DNAKIT.md
others/skills/adaptations/ena-database/SKILL.md
others/skills/adaptations/ena-database/UPSTREAM.md
others/skills/adaptations/encode-ccres-database/DNAKIT.md
others/skills/adaptations/encode-ccres-database/SKILL.md
others/skills/adaptations/encode-ccres-database/UPSTREAM.md
others/skills/adaptations/encode-database/DNAKIT.md
others/skills/adaptations/encode-database/SKILL.md
others/skills/adaptations/encode-database/UPSTREAM.md
others/skills/adaptations/encode-toolkit-setup/DNAKIT.md
others/skills/adaptations/encode-toolkit-setup/SKILL.md
others/skills/adaptations/encode-toolkit-setup/UPSTREAM.md
others/skills/adaptations/encode-toolkit-setup/references/literature.md
others/skills/adaptations/ensembl-rest/DNAKIT.md
others/skills/adaptations/ensembl-rest/SKILL.md
others/skills/adaptations/ensembl-rest/UPSTREAM.md
others/skills/adaptations/entrez-fetch/DNAKIT.md
others/skills/adaptations/entrez-fetch/SKILL.md
others/skills/adaptations/entrez-fetch/UPSTREAM.md
others/skills/adaptations/entrez-link/DNAKIT.md
others/skills/adaptations/entrez-link/SKILL.md
others/skills/adaptations/entrez-link/UPSTREAM.md
others/skills/adaptations/entrez-search/DNAKIT.md
others/skills/adaptations/entrez-search/SKILL.md
others/skills/adaptations/entrez-search/UPSTREAM.md
others/skills/adaptations/epidemiological-genomics-amr-surveillance/DNAKIT.md
others/skills/adaptations/epidemiological-genomics-amr-surveillance/SKILL.md
others/skills/adaptations/epidemiological-genomics-amr-surveillance/UPSTREAM.md
others/skills/adaptations/epidemiological-genomics-pathogen-typing/DNAKIT.md
others/skills/adaptations/epidemiological-genomics-pathogen-typing/SKILL.md
others/skills/adaptations/epidemiological-genomics-pathogen-typing/UPSTREAM.md
others/skills/adaptations/epidemiological-genomics-phylodynamics/DNAKIT.md
others/skills/adaptations/epidemiological-genomics-phylodynamics/SKILL.md
others/skills/adaptations/epidemiological-genomics-phylodynamics/UPSTREAM.md
others/skills/adaptations/epidemiological-genomics-transmission-inference/DNAKIT.md
others/skills/adaptations/epidemiological-genomics-transmission-inference/SKILL.md
others/skills/adaptations/epidemiological-genomics-transmission-inference/UPSTREAM.md
others/skills/adaptations/epidemiological-genomics-variant-surveillance/DNAKIT.md
others/skills/adaptations/epidemiological-genomics-variant-surveillance/SKILL.md
others/skills/adaptations/epidemiological-genomics-variant-surveillance/UPSTREAM.md
others/skills/adaptations/epigenomics/CODE_REFERENCE.md
others/skills/adaptations/epigenomics/DNAKIT.md
others/skills/adaptations/epigenomics/QUICK_START.md
others/skills/adaptations/epigenomics/SKILL.md
others/skills/adaptations/epigenomics/UPSTREAM.md
others/skills/adaptations/epigenomics/test_skill.py
others/skills/adaptations/epigenomics-chromatin/DNAKIT.md
others/skills/adaptations/epigenomics-chromatin/SKILL.md
others/skills/adaptations/epigenomics-chromatin/UPSTREAM.md
others/skills/adaptations/eqtl-catalogue-region-fetch/DNAKIT.md
others/skills/adaptations/eqtl-catalogue-region-fetch/SKILL.md
others/skills/adaptations/eqtl-catalogue-region-fetch/UPSTREAM.md
others/skills/adaptations/equity-scorer/DNAKIT.md
others/skills/adaptations/equity-scorer/SKILL.md
others/skills/adaptations/equity-scorer/UPSTREAM.md
others/skills/adaptations/equity-scorer/equity_scorer.py
others/skills/adaptations/equity-scorer/tests/test_repro_bundle.py
others/skills/adaptations/erast/DNAKIT.md
others/skills/adaptations/erast/SKILL.md
others/skills/adaptations/erast/UPSTREAM.md
others/skills/adaptations/evo2/DNAKIT.md
others/skills/adaptations/evo2/SKILL.md
others/skills/adaptations/evo2/UPSTREAM.md
others/skills/adaptations/evo2-nim/DNAKIT.md
others/skills/adaptations/evo2-nim/SKILL.md
others/skills/adaptations/evo2-nim/UPSTREAM.md
others/skills/adaptations/experimental-design-batch-design/DNAKIT.md
others/skills/adaptations/experimental-design-batch-design/SKILL.md
others/skills/adaptations/experimental-design-batch-design/UPSTREAM.md
others/skills/adaptations/experimental-design-multiple-testing/DNAKIT.md
others/skills/adaptations/experimental-design-multiple-testing/SKILL.md
others/skills/adaptations/experimental-design-multiple-testing/UPSTREAM.md
others/skills/adaptations/experimental-design-power-analysis/DNAKIT.md
others/skills/adaptations/experimental-design-power-analysis/SKILL.md
others/skills/adaptations/experimental-design-power-analysis/UPSTREAM.md
others/skills/adaptations/experimental-design-randomization-blocking/DNAKIT.md
others/skills/adaptations/experimental-design-randomization-blocking/SKILL.md
others/skills/adaptations/experimental-design-randomization-blocking/UPSTREAM.md
others/skills/adaptations/experimental-design-sample-size/DNAKIT.md
others/skills/adaptations/experimental-design-sample-size/SKILL.md
others/skills/adaptations/experimental-design-sample-size/UPSTREAM.md
others/skills/adaptations/expression-matrix-gene-id-mapping/DNAKIT.md
others/skills/adaptations/expression-matrix-gene-id-mapping/SKILL.md
others/skills/adaptations/expression-matrix-gene-id-mapping/UPSTREAM.md
others/skills/adaptations/fasta-database-curator/DNAKIT.md
others/skills/adaptations/fasta-database-curator/SKILL.md
others/skills/adaptations/fasta-database-curator/UPSTREAM.md
others/skills/adaptations/fastq-quality/DNAKIT.md
others/skills/adaptations/fastq-quality/SKILL.md
others/skills/adaptations/fastq-quality/UPSTREAM.md
others/skills/adaptations/fegenie/DNAKIT.md
others/skills/adaptations/fegenie/SKILL.md
others/skills/adaptations/fegenie/UPSTREAM.md
others/skills/adaptations/filter-sequences/DNAKIT.md
others/skills/adaptations/filter-sequences/SKILL.md
others/skills/adaptations/filter-sequences/UPSTREAM.md
others/skills/adaptations/find-variant-literature/DNAKIT.md
others/skills/adaptations/find-variant-literature/SKILL.md
others/skills/adaptations/find-variant-literature/UPSTREAM.md
others/skills/adaptations/folklore-variant-evidence/DNAKIT.md
others/skills/adaptations/folklore-variant-evidence/SKILL.md
others/skills/adaptations/folklore-variant-evidence/UPSTREAM.md
others/skills/adaptations/format-conversion/DNAKIT.md
others/skills/adaptations/format-conversion/SKILL.md
others/skills/adaptations/format-conversion/UPSTREAM.md
others/skills/adaptations/foundation-housekeeping/DNAKIT.md
others/skills/adaptations/foundation-housekeeping/SKILL.md
others/skills/adaptations/foundation-housekeeping/UPSTREAM.md
others/skills/adaptations/foundation-housekeeping/docs/README.md
others/skills/adaptations/foundation-housekeeping/scripts/build_metadata_catalog.py
others/skills/adaptations/foundation-housekeeping/scripts/build_sample_catalog.py
others/skills/adaptations/fragment-analysis/DNAKIT.md
others/skills/adaptations/fragment-analysis/SKILL.md
others/skills/adaptations/fragment-analysis/UPSTREAM.md
others/skills/adaptations/functional-genomics-screens/DNAKIT.md
others/skills/adaptations/functional-genomics-screens/SKILL.md
others/skills/adaptations/functional-genomics-screens/UPSTREAM.md
others/skills/adaptations/functional-screen-analysis/DNAKIT.md
others/skills/adaptations/functional-screen-analysis/SKILL.md
others/skills/adaptations/functional-screen-analysis/UPSTREAM.md
others/skills/adaptations/functional-screen-analysis/references/literature.md
others/skills/adaptations/gatk-variant-calling/DNAKIT.md
others/skills/adaptations/gatk-variant-calling/SKILL.md
others/skills/adaptations/gatk-variant-calling/UPSTREAM.md
others/skills/adaptations/gene-database/DNAKIT.md
others/skills/adaptations/gene-database/SKILL.md
others/skills/adaptations/gene-database/UPSTREAM.md
others/skills/adaptations/gene-disease-association/DNAKIT.md
others/skills/adaptations/gene-disease-association/SKILL.md
others/skills/adaptations/gene-disease-association/UPSTREAM.md
others/skills/adaptations/gene-regulatory-networks/DNAKIT.md
others/skills/adaptations/gene-regulatory-networks/SKILL.md
others/skills/adaptations/gene-regulatory-networks/UPSTREAM.md
others/skills/adaptations/gene-regulatory-networks-multiomics-grn/DNAKIT.md
others/skills/adaptations/gene-regulatory-networks-multiomics-grn/SKILL.md
others/skills/adaptations/gene-regulatory-networks-multiomics-grn/UPSTREAM.md
others/skills/adaptations/gene-regulatory-networks-scenic-regulons/DNAKIT.md
others/skills/adaptations/gene-regulatory-networks-scenic-regulons/SKILL.md
others/skills/adaptations/gene-regulatory-networks-scenic-regulons/UPSTREAM.md
others/skills/adaptations/geniml/DNAKIT.md
others/skills/adaptations/geniml/SKILL.md
others/skills/adaptations/geniml/UPSTREAM.md
others/skills/adaptations/geniml/references/bedspace.md
others/skills/adaptations/geniml/references/consensus_peaks.md
others/skills/adaptations/geniml/references/region2vec.md
others/skills/adaptations/geniml/references/scembed.md
others/skills/adaptations/geniml/references/utilities.md
others/skills/adaptations/genomad/DNAKIT.md
others/skills/adaptations/genomad/SKILL.md
others/skills/adaptations/genomad/UPSTREAM.md
others/skills/adaptations/genome-annotation-annotation-qc/DNAKIT.md
others/skills/adaptations/genome-annotation-annotation-qc/SKILL.md
others/skills/adaptations/genome-annotation-annotation-qc/UPSTREAM.md
others/skills/adaptations/genome-annotation-annotation-transfer/DNAKIT.md
others/skills/adaptations/genome-annotation-annotation-transfer/SKILL.md
others/skills/adaptations/genome-annotation-annotation-transfer/UPSTREAM.md
others/skills/adaptations/genome-annotation-eukaryotic-gene-prediction/DNAKIT.md
others/skills/adaptations/genome-annotation-eukaryotic-gene-prediction/SKILL.md
others/skills/adaptations/genome-annotation-eukaryotic-gene-prediction/UPSTREAM.md
others/skills/adaptations/genome-annotation-functional-annotation/DNAKIT.md
others/skills/adaptations/genome-annotation-functional-annotation/SKILL.md
others/skills/adaptations/genome-annotation-functional-annotation/UPSTREAM.md
others/skills/adaptations/genome-annotation-ncrna-annotation/DNAKIT.md
others/skills/adaptations/genome-annotation-ncrna-annotation/SKILL.md
others/skills/adaptations/genome-annotation-ncrna-annotation/UPSTREAM.md
others/skills/adaptations/genome-annotation-prokaryotic-annotation/DNAKIT.md
others/skills/adaptations/genome-annotation-prokaryotic-annotation/SKILL.md
others/skills/adaptations/genome-annotation-prokaryotic-annotation/UPSTREAM.md
others/skills/adaptations/genome-annotation-repeat-annotation/DNAKIT.md
others/skills/adaptations/genome-annotation-repeat-annotation/SKILL.md
others/skills/adaptations/genome-annotation-repeat-annotation/UPSTREAM.md
others/skills/adaptations/genome-assembly-assembly-polishing/DNAKIT.md
others/skills/adaptations/genome-assembly-assembly-polishing/SKILL.md
others/skills/adaptations/genome-assembly-assembly-polishing/UPSTREAM.md
others/skills/adaptations/genome-assembly-assembly-qc/DNAKIT.md
others/skills/adaptations/genome-assembly-assembly-qc/SKILL.md
others/skills/adaptations/genome-assembly-assembly-qc/UPSTREAM.md
others/skills/adaptations/genome-assembly-contamination-detection/DNAKIT.md
others/skills/adaptations/genome-assembly-contamination-detection/SKILL.md
others/skills/adaptations/genome-assembly-contamination-detection/UPSTREAM.md
others/skills/adaptations/genome-assembly-genome-profiling/DNAKIT.md
others/skills/adaptations/genome-assembly-genome-profiling/SKILL.md
others/skills/adaptations/genome-assembly-genome-profiling/UPSTREAM.md
others/skills/adaptations/genome-assembly-hifi-assembly/DNAKIT.md
others/skills/adaptations/genome-assembly-hifi-assembly/SKILL.md
others/skills/adaptations/genome-assembly-hifi-assembly/UPSTREAM.md
others/skills/adaptations/genome-assembly-long-read-assembly/DNAKIT.md
others/skills/adaptations/genome-assembly-long-read-assembly/SKILL.md
others/skills/adaptations/genome-assembly-long-read-assembly/UPSTREAM.md
others/skills/adaptations/genome-assembly-metagenome-assembly/DNAKIT.md
others/skills/adaptations/genome-assembly-metagenome-assembly/SKILL.md
others/skills/adaptations/genome-assembly-metagenome-assembly/UPSTREAM.md
others/skills/adaptations/genome-assembly-scaffolding/DNAKIT.md
others/skills/adaptations/genome-assembly-scaffolding/SKILL.md
others/skills/adaptations/genome-assembly-scaffolding/UPSTREAM.md
others/skills/adaptations/genome-assembly-short-read-assembly/DNAKIT.md
others/skills/adaptations/genome-assembly-short-read-assembly/SKILL.md
others/skills/adaptations/genome-assembly-short-read-assembly/UPSTREAM.md
others/skills/adaptations/genome-engineering-base-editing-design/DNAKIT.md
others/skills/adaptations/genome-engineering-base-editing-design/SKILL.md
others/skills/adaptations/genome-engineering-base-editing-design/UPSTREAM.md
others/skills/adaptations/genome-engineering-grna-design/DNAKIT.md
others/skills/adaptations/genome-engineering-grna-design/SKILL.md
others/skills/adaptations/genome-engineering-grna-design/UPSTREAM.md
others/skills/adaptations/genome-engineering-hdr-template-design/DNAKIT.md
others/skills/adaptations/genome-engineering-hdr-template-design/SKILL.md
others/skills/adaptations/genome-engineering-hdr-template-design/UPSTREAM.md
others/skills/adaptations/genome-engineering-off-target-prediction/DNAKIT.md
others/skills/adaptations/genome-engineering-off-target-prediction/SKILL.md
others/skills/adaptations/genome-engineering-off-target-prediction/UPSTREAM.md
others/skills/adaptations/genome-engineering-prime-editing-design/DNAKIT.md
others/skills/adaptations/genome-engineering-prime-editing-design/SKILL.md
others/skills/adaptations/genome-engineering-prime-editing-design/UPSTREAM.md
others/skills/adaptations/genome-intervals-bed-file-basics/DNAKIT.md
others/skills/adaptations/genome-intervals-bed-file-basics/SKILL.md
others/skills/adaptations/genome-intervals-bed-file-basics/UPSTREAM.md
others/skills/adaptations/genome-intervals-bedgraph-handling/DNAKIT.md
others/skills/adaptations/genome-intervals-bedgraph-handling/SKILL.md
others/skills/adaptations/genome-intervals-bedgraph-handling/UPSTREAM.md
others/skills/adaptations/genome-intervals-bigwig-tracks/DNAKIT.md
others/skills/adaptations/genome-intervals-bigwig-tracks/SKILL.md
others/skills/adaptations/genome-intervals-bigwig-tracks/UPSTREAM.md
others/skills/adaptations/genome-intervals-coverage-analysis/DNAKIT.md
others/skills/adaptations/genome-intervals-coverage-analysis/SKILL.md
others/skills/adaptations/genome-intervals-coverage-analysis/UPSTREAM.md
others/skills/adaptations/genome-intervals-gtf-gff-handling/DNAKIT.md
others/skills/adaptations/genome-intervals-gtf-gff-handling/SKILL.md
others/skills/adaptations/genome-intervals-gtf-gff-handling/UPSTREAM.md
others/skills/adaptations/genome-intervals-interval-arithmetic/DNAKIT.md
others/skills/adaptations/genome-intervals-interval-arithmetic/SKILL.md
others/skills/adaptations/genome-intervals-interval-arithmetic/UPSTREAM.md
others/skills/adaptations/genome-intervals-overlap-significance/DNAKIT.md
others/skills/adaptations/genome-intervals-overlap-significance/SKILL.md
others/skills/adaptations/genome-intervals-overlap-significance/UPSTREAM.md
others/skills/adaptations/genome-intervals-proximity-operations/DNAKIT.md
others/skills/adaptations/genome-intervals-proximity-operations/SKILL.md
others/skills/adaptations/genome-intervals-proximity-operations/UPSTREAM.md
others/skills/adaptations/genome-language-model/DNAKIT.md
others/skills/adaptations/genome-language-model/SKILL.md
others/skills/adaptations/genome-language-model/UPSTREAM.md
others/skills/adaptations/genomic-coordinates/DNAKIT.md
others/skills/adaptations/genomic-coordinates/SKILL.md
others/skills/adaptations/genomic-coordinates/UPSTREAM.md
others/skills/adaptations/genomic-intelligence/DNAKIT.md
others/skills/adaptations/genomic-intelligence/SKILL.md
others/skills/adaptations/genomic-intelligence/UPSTREAM.md
others/skills/adaptations/genomics-study-design/DNAKIT.md
others/skills/adaptations/genomics-study-design/SKILL.md
others/skills/adaptations/genomics-study-design/UPSTREAM.md
others/skills/adaptations/genomics-workflow-acceleration/DNAKIT.md
others/skills/adaptations/genomics-workflow-acceleration/SKILL.md
others/skills/adaptations/genomics-workflow-acceleration/UPSTREAM.md
others/skills/adaptations/genomics-workflow-acceleration/references/parabricks-runtime-readiness.md
others/skills/adaptations/genotype-imputation-benchmarking/DNAKIT.md
others/skills/adaptations/genotype-imputation-benchmarking/SKILL.md
others/skills/adaptations/genotype-imputation-benchmarking/UPSTREAM.md
others/skills/adaptations/geo-data/DNAKIT.md
others/skills/adaptations/geo-data/SKILL.md
others/skills/adaptations/geo-data/UPSTREAM.md
others/skills/adaptations/gget-genomic-databases/DNAKIT.md
others/skills/adaptations/gget-genomic-databases/SKILL.md
others/skills/adaptations/gget-genomic-databases/UPSTREAM.md
others/skills/adaptations/grapevine-adna/DNAKIT.md
others/skills/adaptations/grapevine-adna/SKILL.md
others/skills/adaptations/grapevine-adna/UPSTREAM.md
others/skills/adaptations/gtdb/DNAKIT.md
others/skills/adaptations/gtdb/SKILL.md
others/skills/adaptations/gtdb/UPSTREAM.md
others/skills/adaptations/gtex-database/DNAKIT.md
others/skills/adaptations/gtex-database/SKILL.md
others/skills/adaptations/gtex-database/UPSTREAM.md
others/skills/adaptations/gunc/DNAKIT.md
others/skills/adaptations/gunc/SKILL.md
others/skills/adaptations/gunc/UPSTREAM.md
others/skills/adaptations/gwas-catalog-region-fetch/DNAKIT.md
others/skills/adaptations/gwas-catalog-region-fetch/SKILL.md
others/skills/adaptations/gwas-catalog-region-fetch/UPSTREAM.md
others/skills/adaptations/gwas-database/DNAKIT.md
others/skills/adaptations/gwas-database/SKILL.md
others/skills/adaptations/gwas-database/UPSTREAM.md
others/skills/adaptations/gwas-drug-discovery/DNAKIT.md
others/skills/adaptations/gwas-drug-discovery/QUICK_START.md
others/skills/adaptations/gwas-drug-discovery/SKILL.md
others/skills/adaptations/gwas-drug-discovery/UPSTREAM.md
others/skills/adaptations/gwas-drug-discovery/python_implementation.py
others/skills/adaptations/gwas-drug-discovery/test_gwas_drug_tools.py
others/skills/adaptations/gwas-drug-discovery/test_gwas_drug_tools_v2.py
others/skills/adaptations/gwas-snp-interpretation/DNAKIT.md
others/skills/adaptations/gwas-snp-interpretation/QUICK_START.md
others/skills/adaptations/gwas-snp-interpretation/SKILL.md
others/skills/adaptations/gwas-snp-interpretation/UPSTREAM.md
others/skills/adaptations/gwas-snp-interpretation/python_implementation.py
others/skills/adaptations/gwas-snp-interpretation/test_gwas_snp_tools.py
others/skills/adaptations/gwas-snp-interpretation/test_gwas_snp_tools_simple.py
others/skills/adaptations/gwas-snp-interpretation/test_skill_comprehensive.py
others/skills/adaptations/gwas-trait-to-gene/DNAKIT.md
others/skills/adaptations/gwas-trait-to-gene/SKILL.md
others/skills/adaptations/gwas-trait-to-gene/UPSTREAM.md
others/skills/adaptations/gwas-trait-to-gene/python_implementation.py
others/skills/adaptations/gwas-trait-to-gene/test_gwas_tools.py
others/skills/adaptations/gwas-trait-to-gene/test_skill_comprehensive.py
others/skills/adaptations/hadeg/DNAKIT.md
others/skills/adaptations/hadeg/SKILL.md
others/skills/adaptations/hadeg/UPSTREAM.md
others/skills/adaptations/hi-c-analysis-compartment-analysis/DNAKIT.md
others/skills/adaptations/hi-c-analysis-compartment-analysis/SKILL.md
others/skills/adaptations/hi-c-analysis-compartment-analysis/UPSTREAM.md
others/skills/adaptations/hi-c-analysis-contact-pairs/DNAKIT.md
others/skills/adaptations/hi-c-analysis-contact-pairs/SKILL.md
others/skills/adaptations/hi-c-analysis-contact-pairs/UPSTREAM.md
others/skills/adaptations/hi-c-analysis-hic-data-io/DNAKIT.md
others/skills/adaptations/hi-c-analysis-hic-data-io/SKILL.md
others/skills/adaptations/hi-c-analysis-hic-data-io/UPSTREAM.md
others/skills/adaptations/hi-c-analysis-hic-differential/DNAKIT.md
others/skills/adaptations/hi-c-analysis-hic-differential/SKILL.md
others/skills/adaptations/hi-c-analysis-hic-differential/UPSTREAM.md
others/skills/adaptations/hi-c-analysis-hic-visualization/DNAKIT.md
others/skills/adaptations/hi-c-analysis-hic-visualization/SKILL.md
others/skills/adaptations/hi-c-analysis-hic-visualization/UPSTREAM.md
others/skills/adaptations/hi-c-analysis-hichip-plac-loops/DNAKIT.md
others/skills/adaptations/hi-c-analysis-hichip-plac-loops/SKILL.md
others/skills/adaptations/hi-c-analysis-hichip-plac-loops/UPSTREAM.md
others/skills/adaptations/hi-c-analysis-loop-calling/DNAKIT.md
others/skills/adaptations/hi-c-analysis-loop-calling/SKILL.md
others/skills/adaptations/hi-c-analysis-loop-calling/UPSTREAM.md
others/skills/adaptations/hi-c-analysis-matrix-operations/DNAKIT.md
others/skills/adaptations/hi-c-analysis-matrix-operations/SKILL.md
others/skills/adaptations/hi-c-analysis-matrix-operations/UPSTREAM.md
others/skills/adaptations/hi-c-analysis-tad-detection/DNAKIT.md
others/skills/adaptations/hi-c-analysis-tad-detection/SKILL.md
others/skills/adaptations/hi-c-analysis-tad-detection/UPSTREAM.md
others/skills/adaptations/hic-aggregation/DNAKIT.md
others/skills/adaptations/hic-aggregation/SKILL.md
others/skills/adaptations/hic-aggregation/UPSTREAM.md
others/skills/adaptations/hic-aggregation/references/literature.md
others/skills/adaptations/hic-aggregation/references/loop-caller-comparison.md
others/skills/adaptations/histone-aggregation/DNAKIT.md
others/skills/adaptations/histone-aggregation/SKILL.md
others/skills/adaptations/histone-aggregation/UPSTREAM.md
others/skills/adaptations/histone-aggregation/references/broad-vs-narrow.md
others/skills/adaptations/histone-aggregation/references/histone-marks-reference.md
others/skills/adaptations/histone-aggregation/references/literature.md
others/skills/adaptations/histone-aggregation/references/signal-filtering.md
others/skills/adaptations/hla-immunogenomics/DNAKIT.md
others/skills/adaptations/hla-immunogenomics/SKILL.md
others/skills/adaptations/hla-immunogenomics/UPSTREAM.md
others/skills/adaptations/illumina-bridge/DNAKIT.md
others/skills/adaptations/illumina-bridge/SKILL.md
others/skills/adaptations/illumina-bridge/UPSTREAM.md
others/skills/adaptations/illumina-bridge/illumina_bridge.py
others/skills/adaptations/immune-repertoire-analysis/ANALYSIS_DETAILS.md
others/skills/adaptations/immune-repertoire-analysis/DNAKIT.md
others/skills/adaptations/immune-repertoire-analysis/SKILL.md
others/skills/adaptations/immune-repertoire-analysis/UPSTREAM.md
others/skills/adaptations/immunoinformatics-epitope-prediction/DNAKIT.md
others/skills/adaptations/immunoinformatics-epitope-prediction/SKILL.md
others/skills/adaptations/immunoinformatics-epitope-prediction/UPSTREAM.md
others/skills/adaptations/immunoinformatics-immunogenicity-scoring/DNAKIT.md
others/skills/adaptations/immunoinformatics-immunogenicity-scoring/SKILL.md
others/skills/adaptations/immunoinformatics-immunogenicity-scoring/UPSTREAM.md
others/skills/adaptations/immunoinformatics-mhc-binding-prediction/DNAKIT.md
others/skills/adaptations/immunoinformatics-mhc-binding-prediction/SKILL.md
others/skills/adaptations/immunoinformatics-mhc-binding-prediction/UPSTREAM.md
others/skills/adaptations/immunoinformatics-mhc-class-ii-prediction/DNAKIT.md
others/skills/adaptations/immunoinformatics-mhc-class-ii-prediction/SKILL.md
others/skills/adaptations/immunoinformatics-mhc-class-ii-prediction/UPSTREAM.md
others/skills/adaptations/immunoinformatics-neoantigen-prediction/DNAKIT.md
others/skills/adaptations/immunoinformatics-neoantigen-prediction/SKILL.md
others/skills/adaptations/immunoinformatics-neoantigen-prediction/UPSTREAM.md
others/skills/adaptations/importing-tracks/DNAKIT.md
others/skills/adaptations/importing-tracks/SKILL.md
others/skills/adaptations/importing-tracks/UPSTREAM.md
others/skills/adaptations/insilicoseq/DNAKIT.md
others/skills/adaptations/insilicoseq/SKILL.md
others/skills/adaptations/insilicoseq/UPSTREAM.md
others/skills/adaptations/integronfinder/DNAKIT.md
others/skills/adaptations/integronfinder/SKILL.md
others/skills/adaptations/integronfinder/UPSTREAM.md
others/skills/adaptations/interdomain-hgt/DNAKIT.md
others/skills/adaptations/interdomain-hgt/SKILL.md
others/skills/adaptations/interdomain-hgt/UPSTREAM.md
others/skills/adaptations/interdomain-hgt/docs/README.md
others/skills/adaptations/interdomain-hgt/docs/database-availability.md
others/skills/adaptations/interdomain-hgt/scripts/run_hgt_evidence.py
others/skills/adaptations/interpret-negative-or-vus/DNAKIT.md
others/skills/adaptations/interpret-negative-or-vus/SKILL.md
others/skills/adaptations/interpret-negative-or-vus/UPSTREAM.md
others/skills/adaptations/isabl-debug-analysis/DNAKIT.md
others/skills/adaptations/isabl-debug-analysis/SKILL.md
others/skills/adaptations/isabl-debug-analysis/UPSTREAM.md
others/skills/adaptations/isabl-merge-results/DNAKIT.md
others/skills/adaptations/isabl-merge-results/SKILL.md
others/skills/adaptations/isabl-merge-results/UPSTREAM.md
others/skills/adaptations/isabl-monitor-analyses/DNAKIT.md
others/skills/adaptations/isabl-monitor-analyses/SKILL.md
others/skills/adaptations/isabl-monitor-analyses/UPSTREAM.md
others/skills/adaptations/isabl-project-report/DNAKIT.md
others/skills/adaptations/isabl-project-report/SKILL.md
others/skills/adaptations/isabl-project-report/UPSTREAM.md
others/skills/adaptations/isabl-query-data/DNAKIT.md
others/skills/adaptations/isabl-query-data/SKILL.md
others/skills/adaptations/isabl-query-data/UPSTREAM.md
others/skills/adaptations/isabl-run-pipeline/DNAKIT.md
others/skills/adaptations/isabl-run-pipeline/SKILL.md
others/skills/adaptations/isabl-run-pipeline/UPSTREAM.md
others/skills/adaptations/isabl-submit-data/DNAKIT.md
others/skills/adaptations/isabl-submit-data/SKILL.md
others/skills/adaptations/isabl-submit-data/UPSTREAM.md
others/skills/adaptations/isabl-write-app/DNAKIT.md
others/skills/adaptations/isabl-write-app/SKILL.md
others/skills/adaptations/isabl-write-app/UPSTREAM.md
others/skills/adaptations/isescan/DNAKIT.md
others/skills/adaptations/isescan/SKILL.md
others/skills/adaptations/isescan/UPSTREAM.md
others/skills/adaptations/jaspar-database/DNAKIT.md
others/skills/adaptations/jaspar-database/SKILL.md
others/skills/adaptations/jaspar-database/UPSTREAM.md
others/skills/adaptations/ld-1000g-region-compute/DNAKIT.md
others/skills/adaptations/ld-1000g-region-compute/SKILL.md
others/skills/adaptations/ld-1000g-region-compute/UPSTREAM.md
others/skills/adaptations/lexicmap/DNAKIT.md
others/skills/adaptations/lexicmap/SKILL.md
others/skills/adaptations/lexicmap/UPSTREAM.md
others/skills/adaptations/liftover-coordinates/DNAKIT.md
others/skills/adaptations/liftover-coordinates/SKILL.md
others/skills/adaptations/liftover-coordinates/UPSTREAM.md
others/skills/adaptations/liftover-coordinates/references/literature.md
others/skills/adaptations/local-blast/DNAKIT.md
others/skills/adaptations/local-blast/SKILL.md
others/skills/adaptations/local-blast/UPSTREAM.md
others/skills/adaptations/locuscompare-region-render/DNAKIT.md
others/skills/adaptations/locuscompare-region-render/SKILL.md
others/skills/adaptations/locuscompare-region-render/UPSTREAM.md
others/skills/adaptations/locuscompare-region-render/commands.sh
others/skills/adaptations/locuscompare-region-render/examples/01_synthetic_demo/README.md
others/skills/adaptations/locuscompare-region-render/examples/02_eqtl_catalogue_x_gwas_catalog/README.md
others/skills/adaptations/locuscompare-region-render/examples/03_open_targets_followup/README.md
others/skills/adaptations/locuscompare-region-render/examples/04_gwas_lookup_followup/README.md
others/skills/adaptations/locuscompare-region-render/examples/05_sqtl_sort1_liver_txrev/README.md
others/skills/adaptations/locuscompare-region-render/examples/06_sceqtl_sort1_onek1k_cd14_mono/README.md
others/skills/adaptations/locuscompare-region-render/examples/07_pqtl_sort1_ukbppp_eur/README.md
others/skills/adaptations/locuscompare-region-render/examples/chains/finemapping_chain/README.md
others/skills/adaptations/long-read-sequencing-basecalling/DNAKIT.md
others/skills/adaptations/long-read-sequencing-basecalling/SKILL.md
others/skills/adaptations/long-read-sequencing-basecalling/UPSTREAM.md
others/skills/adaptations/long-read-sequencing-clair3-variants/DNAKIT.md
others/skills/adaptations/long-read-sequencing-clair3-variants/SKILL.md
others/skills/adaptations/long-read-sequencing-clair3-variants/UPSTREAM.md
others/skills/adaptations/long-read-sequencing-haplotype-phasing/DNAKIT.md
others/skills/adaptations/long-read-sequencing-haplotype-phasing/SKILL.md
others/skills/adaptations/long-read-sequencing-haplotype-phasing/UPSTREAM.md
others/skills/adaptations/long-read-sequencing-long-read-alignment/DNAKIT.md
others/skills/adaptations/long-read-sequencing-long-read-alignment/SKILL.md
others/skills/adaptations/long-read-sequencing-long-read-alignment/UPSTREAM.md
others/skills/adaptations/long-read-sequencing-long-read-qc/DNAKIT.md
others/skills/adaptations/long-read-sequencing-long-read-qc/SKILL.md
others/skills/adaptations/long-read-sequencing-long-read-qc/UPSTREAM.md
others/skills/adaptations/long-read-sequencing-medaka-polishing/DNAKIT.md
others/skills/adaptations/long-read-sequencing-medaka-polishing/SKILL.md
others/skills/adaptations/long-read-sequencing-medaka-polishing/UPSTREAM.md
others/skills/adaptations/long-read-sequencing-nanopore-methylation/DNAKIT.md
others/skills/adaptations/long-read-sequencing-nanopore-methylation/SKILL.md
others/skills/adaptations/long-read-sequencing-nanopore-methylation/UPSTREAM.md
others/skills/adaptations/long-read-sequencing-structural-variants/DNAKIT.md
others/skills/adaptations/long-read-sequencing-structural-variants/SKILL.md
others/skills/adaptations/long-read-sequencing-structural-variants/UPSTREAM.md
others/skills/adaptations/longitudinal-monitoring/DNAKIT.md
others/skills/adaptations/longitudinal-monitoring/SKILL.md
others/skills/adaptations/longitudinal-monitoring/UPSTREAM.md
others/skills/adaptations/lorbin/DNAKIT.md
others/skills/adaptations/lorbin/SKILL.md
others/skills/adaptations/lorbin/UPSTREAM.md
others/skills/adaptations/mebs/DNAKIT.md
others/skills/adaptations/mebs/SKILL.md
others/skills/adaptations/mebs/UPSTREAM.md
others/skills/adaptations/metabat2/DNAKIT.md
others/skills/adaptations/metabat2/SKILL.md
others/skills/adaptations/metabat2/UPSTREAM.md
others/skills/adaptations/metabolic/DNAKIT.md
others/skills/adaptations/metabolic/SKILL.md
others/skills/adaptations/metabolic/UPSTREAM.md
others/skills/adaptations/metagenomics-abundance/DNAKIT.md
others/skills/adaptations/metagenomics-abundance/SKILL.md
others/skills/adaptations/metagenomics-abundance/UPSTREAM.md
others/skills/adaptations/metagenomics-amr-detection/DNAKIT.md
others/skills/adaptations/metagenomics-amr-detection/SKILL.md
others/skills/adaptations/metagenomics-amr-detection/UPSTREAM.md
others/skills/adaptations/metagenomics-contamination-controls/DNAKIT.md
others/skills/adaptations/metagenomics-contamination-controls/SKILL.md
others/skills/adaptations/metagenomics-contamination-controls/UPSTREAM.md
others/skills/adaptations/metagenomics-functional-profiling/DNAKIT.md
others/skills/adaptations/metagenomics-functional-profiling/SKILL.md
others/skills/adaptations/metagenomics-functional-profiling/UPSTREAM.md
others/skills/adaptations/metagenomics-kraken/DNAKIT.md
others/skills/adaptations/metagenomics-kraken/SKILL.md
others/skills/adaptations/metagenomics-kraken/UPSTREAM.md
others/skills/adaptations/metagenomics-metaphlan/DNAKIT.md
others/skills/adaptations/metagenomics-metaphlan/SKILL.md
others/skills/adaptations/metagenomics-metaphlan/UPSTREAM.md
others/skills/adaptations/metagenomics-strain-tracking/DNAKIT.md
others/skills/adaptations/metagenomics-strain-tracking/SKILL.md
others/skills/adaptations/metagenomics-strain-tracking/UPSTREAM.md
others/skills/adaptations/metagenomics-visualization/DNAKIT.md
others/skills/adaptations/metagenomics-visualization/SKILL.md
others/skills/adaptations/metagenomics-visualization/UPSTREAM.md
others/skills/adaptations/methylation-aggregation/DNAKIT.md
others/skills/adaptations/methylation-aggregation/SKILL.md
others/skills/adaptations/methylation-aggregation/UPSTREAM.md
others/skills/adaptations/methylation-aggregation/references/hmr-definitions.md
others/skills/adaptations/methylation-aggregation/references/literature.md
others/skills/adaptations/methylation-array-preprocessing/DNAKIT.md
others/skills/adaptations/methylation-array-preprocessing/SKILL.md
others/skills/adaptations/methylation-array-preprocessing/UPSTREAM.md
others/skills/adaptations/methylation-array-qc-filtering/DNAKIT.md
others/skills/adaptations/methylation-array-qc-filtering/SKILL.md
others/skills/adaptations/methylation-array-qc-filtering/UPSTREAM.md
others/skills/adaptations/methylation-based-detection/DNAKIT.md
others/skills/adaptations/methylation-based-detection/SKILL.md
others/skills/adaptations/methylation-based-detection/UPSTREAM.md
others/skills/adaptations/methylation-bismark-alignment/DNAKIT.md
others/skills/adaptations/methylation-bismark-alignment/SKILL.md
others/skills/adaptations/methylation-bismark-alignment/UPSTREAM.md
others/skills/adaptations/methylation-calling/DNAKIT.md
others/skills/adaptations/methylation-calling/SKILL.md
others/skills/adaptations/methylation-calling/UPSTREAM.md
others/skills/adaptations/methylation-cell-type-deconvolution/DNAKIT.md
others/skills/adaptations/methylation-cell-type-deconvolution/SKILL.md
others/skills/adaptations/methylation-cell-type-deconvolution/UPSTREAM.md
others/skills/adaptations/methylation-differential-cpg/DNAKIT.md
others/skills/adaptations/methylation-differential-cpg/SKILL.md
others/skills/adaptations/methylation-differential-cpg/UPSTREAM.md
others/skills/adaptations/methylation-dmr-detection/DNAKIT.md
others/skills/adaptations/methylation-dmr-detection/SKILL.md
others/skills/adaptations/methylation-dmr-detection/UPSTREAM.md
others/skills/adaptations/methylation-epigenetic-clocks/DNAKIT.md
others/skills/adaptations/methylation-epigenetic-clocks/SKILL.md
others/skills/adaptations/methylation-epigenetic-clocks/UPSTREAM.md
others/skills/adaptations/methylation-ewas-design/DNAKIT.md
others/skills/adaptations/methylation-ewas-design/SKILL.md
others/skills/adaptations/methylation-ewas-design/UPSTREAM.md
others/skills/adaptations/methylation-methylkit/DNAKIT.md
others/skills/adaptations/methylation-methylkit/SKILL.md
others/skills/adaptations/methylation-methylkit/UPSTREAM.md
others/skills/adaptations/mgnify/DNAKIT.md
others/skills/adaptations/mgnify/SKILL.md
others/skills/adaptations/mgnify/UPSTREAM.md
others/skills/adaptations/microbial-genome-characterization/DNAKIT.md
others/skills/adaptations/microbial-genome-characterization/SKILL.md
others/skills/adaptations/microbial-genome-characterization/UPSTREAM.md
others/skills/adaptations/microbial-genome-characterization/evals/evals.json
others/skills/adaptations/microbial-mining/DNAKIT.md
others/skills/adaptations/microbial-mining/SKILL.md
others/skills/adaptations/microbial-mining/UPSTREAM.md
others/skills/adaptations/microbiome-amplicon-processing/DNAKIT.md
others/skills/adaptations/microbiome-amplicon-processing/SKILL.md
others/skills/adaptations/microbiome-amplicon-processing/UPSTREAM.md
others/skills/adaptations/microbiome-differential-abundance/DNAKIT.md
others/skills/adaptations/microbiome-differential-abundance/SKILL.md
others/skills/adaptations/microbiome-differential-abundance/UPSTREAM.md
others/skills/adaptations/microbiome-diversity-analysis/DNAKIT.md
others/skills/adaptations/microbiome-diversity-analysis/SKILL.md
others/skills/adaptations/microbiome-diversity-analysis/UPSTREAM.md
others/skills/adaptations/microbiome-functional-prediction/DNAKIT.md
others/skills/adaptations/microbiome-functional-prediction/SKILL.md
others/skills/adaptations/microbiome-functional-prediction/UPSTREAM.md
others/skills/adaptations/microbiome-qiime2-workflow/DNAKIT.md
others/skills/adaptations/microbiome-qiime2-workflow/SKILL.md
others/skills/adaptations/microbiome-qiime2-workflow/UPSTREAM.md
others/skills/adaptations/microbiome-research/DNAKIT.md
others/skills/adaptations/microbiome-research/SKILL.md
others/skills/adaptations/microbiome-research/UPSTREAM.md
others/skills/adaptations/microbiome-taxonomy-assignment/DNAKIT.md
others/skills/adaptations/microbiome-taxonomy-assignment/SKILL.md
others/skills/adaptations/microbiome-taxonomy-assignment/UPSTREAM.md
others/skills/adaptations/mob-suite/DNAKIT.md
others/skills/adaptations/mob-suite/SKILL.md
others/skills/adaptations/mob-suite/UPSTREAM.md
others/skills/adaptations/mobileelementfinder/DNAKIT.md
others/skills/adaptations/mobileelementfinder/SKILL.md
others/skills/adaptations/mobileelementfinder/UPSTREAM.md
others/skills/adaptations/mobileog/DNAKIT.md
others/skills/adaptations/mobileog/SKILL.md
others/skills/adaptations/mobileog/UPSTREAM.md
others/skills/adaptations/model-organism-genetics/DNAKIT.md
others/skills/adaptations/model-organism-genetics/SKILL.md
others/skills/adaptations/model-organism-genetics/UPSTREAM.md
others/skills/adaptations/molecular-cloning/DNAKIT.md
others/skills/adaptations/molecular-cloning/SKILL.md
others/skills/adaptations/molecular-cloning/UPSTREAM.md
others/skills/adaptations/molecular-cloning/scripts/cloning_qc.py
others/skills/adaptations/monarch-database/DNAKIT.md
others/skills/adaptations/monarch-database/SKILL.md
others/skills/adaptations/monarch-database/UPSTREAM.md
others/skills/adaptations/motif-search/DNAKIT.md
others/skills/adaptations/motif-search/SKILL.md
others/skills/adaptations/motif-search/UPSTREAM.md
others/skills/adaptations/mouse-phenome-database/DNAKIT.md
others/skills/adaptations/mouse-phenome-database/SKILL.md
others/skills/adaptations/mouse-phenome-database/UPSTREAM.md
others/skills/adaptations/multi-omics-data-harmonization/DNAKIT.md
others/skills/adaptations/multi-omics-data-harmonization/SKILL.md
others/skills/adaptations/multi-omics-data-harmonization/UPSTREAM.md
others/skills/adaptations/multi-omics-integration/DNAKIT.md
others/skills/adaptations/multi-omics-integration/SKILL.md
others/skills/adaptations/multi-omics-integration/UPSTREAM.md
others/skills/adaptations/multi-omics-integration/phase_details.md
others/skills/adaptations/multi-omics-mixomics-analysis/DNAKIT.md
others/skills/adaptations/multi-omics-mixomics-analysis/SKILL.md
others/skills/adaptations/multi-omics-mixomics-analysis/UPSTREAM.md
others/skills/adaptations/multi-omics-mofa-integration/DNAKIT.md
others/skills/adaptations/multi-omics-mofa-integration/SKILL.md
others/skills/adaptations/multi-omics-mofa-integration/UPSTREAM.md
others/skills/adaptations/multiomic-disease-characterization/DNAKIT.md
others/skills/adaptations/multiomic-disease-characterization/SKILL.md
others/skills/adaptations/multiomic-disease-characterization/UPSTREAM.md
others/skills/adaptations/multiomic-disease-characterization/test_multiomic_disease.py
others/skills/adaptations/multiqc-reporter/DNAKIT.md
others/skills/adaptations/multiqc-reporter/SKILL.md
others/skills/adaptations/multiqc-reporter/UPSTREAM.md
others/skills/adaptations/multiqc-reporter/multiqc_reporter.py
others/skills/adaptations/ncbi-datasets-cli/DNAKIT.md
others/skills/adaptations/ncbi-datasets-cli/SKILL.md
others/skills/adaptations/ncbi-datasets-cli/UPSTREAM.md
others/skills/adaptations/nfcore-sarek-wrapper/CHANGELOG.md
others/skills/adaptations/nfcore-sarek-wrapper/DNAKIT.md
others/skills/adaptations/nfcore-sarek-wrapper/README.md
others/skills/adaptations/nfcore-sarek-wrapper/SKILL.md
others/skills/adaptations/nfcore-sarek-wrapper/UPSTREAM.md
others/skills/adaptations/nfcore-sarek-wrapper/nfcore_sarek_wrapper.py
others/skills/adaptations/nfcore-sarek-wrapper/params_builder.py
others/skills/adaptations/nfcore-sarek-wrapper/provenance.py
others/skills/adaptations/nfcore-sarek-wrapper/remap_paths.py
others/skills/adaptations/nfcore-sarek-wrapper/reporting.py
others/skills/adaptations/nfcore-sarek-wrapper/demo/README.md
others/skills/adaptations/nfcore-sarek-wrapper/tests/test_cli_direct_invocation.py
others/skills/adaptations/ngs-tertiary-analysis/DNAKIT.md
others/skills/adaptations/ngs-tertiary-analysis/SKILL.md
others/skills/adaptations/ngs-tertiary-analysis/UPSTREAM.md
others/skills/adaptations/nucleotide-transformer/DNAKIT.md
others/skills/adaptations/nucleotide-transformer/SKILL.md
others/skills/adaptations/nucleotide-transformer/UPSTREAM.md
others/skills/adaptations/omg/DNAKIT.md
others/skills/adaptations/omg/SKILL.md
others/skills/adaptations/omg/UPSTREAM.md
others/skills/adaptations/optimize-hifi-diploid-assembly/DNAKIT.md
others/skills/adaptations/optimize-hifi-diploid-assembly/SKILL.md
others/skills/adaptations/optimize-hifi-diploid-assembly/UPSTREAM.md
others/skills/adaptations/ortholog-inference/DNAKIT.md
others/skills/adaptations/ortholog-inference/SKILL.md
others/skills/adaptations/ortholog-inference/UPSTREAM.md
others/skills/adaptations/paired-end-fastq/DNAKIT.md
others/skills/adaptations/paired-end-fastq/SKILL.md
others/skills/adaptations/paired-end-fastq/UPSTREAM.md
others/skills/adaptations/parabricks/DNAKIT.md
others/skills/adaptations/parabricks/SKILL.md
others/skills/adaptations/parabricks/UPSTREAM.md
others/skills/adaptations/parabricks/references/runtime-environment.md
others/skills/adaptations/pathogen-variant-surveillance/DNAKIT.md
others/skills/adaptations/pathogen-variant-surveillance/SKILL.md
others/skills/adaptations/pathogen-variant-surveillance/UPSTREAM.md
others/skills/adaptations/pathway-disease-genetics/DNAKIT.md
others/skills/adaptations/pathway-disease-genetics/SKILL.md
others/skills/adaptations/pathway-disease-genetics/UPSTREAM.md
others/skills/adaptations/phasing-imputation-genotype-imputation/DNAKIT.md
others/skills/adaptations/phasing-imputation-genotype-imputation/SKILL.md
others/skills/adaptations/phasing-imputation-genotype-imputation/UPSTREAM.md
others/skills/adaptations/phasing-imputation-haplotype-phasing/DNAKIT.md
others/skills/adaptations/phasing-imputation-haplotype-phasing/SKILL.md
others/skills/adaptations/phasing-imputation-haplotype-phasing/UPSTREAM.md
others/skills/adaptations/phasing-imputation-imputation-qc/DNAKIT.md
others/skills/adaptations/phasing-imputation-imputation-qc/SKILL.md
others/skills/adaptations/phasing-imputation-imputation-qc/UPSTREAM.md
others/skills/adaptations/phasing-imputation-reference-panels/DNAKIT.md
others/skills/adaptations/phasing-imputation-reference-panels/SKILL.md
others/skills/adaptations/phasing-imputation-reference-panels/UPSTREAM.md
others/skills/adaptations/phewas/DNAKIT.md
others/skills/adaptations/phewas/SKILL.md
others/skills/adaptations/phewas/UPSTREAM.md
others/skills/adaptations/phewas/evals/evals.json
others/skills/adaptations/phylign/DNAKIT.md
others/skills/adaptations/phylign/SKILL.md
others/skills/adaptations/phylign/UPSTREAM.md
others/skills/adaptations/phylo-bayesian-inference/DNAKIT.md
others/skills/adaptations/phylo-bayesian-inference/SKILL.md
others/skills/adaptations/phylo-bayesian-inference/UPSTREAM.md
others/skills/adaptations/phylo-distance-calculations/DNAKIT.md
others/skills/adaptations/phylo-distance-calculations/SKILL.md
others/skills/adaptations/phylo-distance-calculations/UPSTREAM.md
others/skills/adaptations/phylo-divergence-dating/DNAKIT.md
others/skills/adaptations/phylo-divergence-dating/SKILL.md
others/skills/adaptations/phylo-divergence-dating/UPSTREAM.md
others/skills/adaptations/phylo-modern-tree-inference/DNAKIT.md
others/skills/adaptations/phylo-modern-tree-inference/SKILL.md
others/skills/adaptations/phylo-modern-tree-inference/UPSTREAM.md
others/skills/adaptations/phylo-species-trees/DNAKIT.md
others/skills/adaptations/phylo-species-trees/SKILL.md
others/skills/adaptations/phylo-species-trees/UPSTREAM.md
others/skills/adaptations/phylo-tree-io/DNAKIT.md
others/skills/adaptations/phylo-tree-io/SKILL.md
others/skills/adaptations/phylo-tree-io/UPSTREAM.md
others/skills/adaptations/phylo-tree-manipulation/DNAKIT.md
others/skills/adaptations/phylo-tree-manipulation/SKILL.md
others/skills/adaptations/phylo-tree-manipulation/UPSTREAM.md
others/skills/adaptations/phylo-tree-visualization/DNAKIT.md
others/skills/adaptations/phylo-tree-visualization/SKILL.md
others/skills/adaptations/phylo-tree-visualization/UPSTREAM.md
others/skills/adaptations/phylogenomics/DNAKIT.md
others/skills/adaptations/phylogenomics/SKILL.md
others/skills/adaptations/phylogenomics/UPSTREAM.md
others/skills/adaptations/phylogenomics/scripts/run_phylogenomics.py
others/skills/adaptations/pileup-generation/DNAKIT.md
others/skills/adaptations/pileup-generation/SKILL.md
others/skills/adaptations/pileup-generation/UPSTREAM.md
others/skills/adaptations/pipeline-dnaseseq/DNAKIT.md
others/skills/adaptations/pipeline-dnaseseq/SKILL.md
others/skills/adaptations/pipeline-dnaseseq/UPSTREAM.md
others/skills/adaptations/pipeline-dnaseseq/references/01-qc-trimming.md
others/skills/adaptations/pipeline-dnaseseq/references/02-alignment.md
others/skills/adaptations/pipeline-dnaseseq/references/03-filtering.md
others/skills/adaptations/pipeline-dnaseseq/references/04-hotspot-calling.md
others/skills/adaptations/pipeline-dnaseseq/references/05-footprinting.md
others/skills/adaptations/pipeline-dnaseseq/references/literature.md
others/skills/adaptations/pipeline-guide/DNAKIT.md
others/skills/adaptations/pipeline-guide/SKILL.md
others/skills/adaptations/pipeline-guide/UPSTREAM.md
others/skills/adaptations/pipeline-guide/references/literature.md
others/skills/adaptations/plannotate-plasmid-annotation/DNAKIT.md
others/skills/adaptations/plannotate-plasmid-annotation/SKILL.md
others/skills/adaptations/plannotate-plasmid-annotation/UPSTREAM.md
others/skills/adaptations/plant-genome-guided-primer-design/DNAKIT.md
others/skills/adaptations/plant-genome-guided-primer-design/SKILL.md
others/skills/adaptations/plant-genome-guided-primer-design/UPSTREAM.md
others/skills/adaptations/plant-genomics/DNAKIT.md
others/skills/adaptations/plant-genomics/SKILL.md
others/skills/adaptations/plant-genomics/UPSTREAM.md
others/skills/adaptations/plant-omics-db/DNAKIT.md
others/skills/adaptations/plant-omics-db/SKILL.md
others/skills/adaptations/plant-omics-db/UPSTREAM.md
others/skills/adaptations/plasmaag/DNAKIT.md
others/skills/adaptations/plasmaag/SKILL.md
others/skills/adaptations/plasmaag/UPSTREAM.md
others/skills/adaptations/pod5/DNAKIT.md
others/skills/adaptations/pod5/SKILL.md
others/skills/adaptations/pod5/UPSTREAM.md
others/skills/adaptations/polyploid-gene-family-cloning/DNAKIT.md
others/skills/adaptations/polyploid-gene-family-cloning/SKILL.md
others/skills/adaptations/polyploid-gene-family-cloning/UPSTREAM.md
others/skills/adaptations/population-genetics-1000genomes/DNAKIT.md
others/skills/adaptations/population-genetics-1000genomes/SKILL.md
others/skills/adaptations/population-genetics-1000genomes/UPSTREAM.md
others/skills/adaptations/population-genetics-association-testing/DNAKIT.md
others/skills/adaptations/population-genetics-association-testing/SKILL.md
others/skills/adaptations/population-genetics-association-testing/UPSTREAM.md
others/skills/adaptations/population-genetics-linkage-disequilibrium/DNAKIT.md
others/skills/adaptations/population-genetics-linkage-disequilibrium/SKILL.md
others/skills/adaptations/population-genetics-linkage-disequilibrium/UPSTREAM.md
others/skills/adaptations/population-genetics-plink-basics/DNAKIT.md
others/skills/adaptations/population-genetics-plink-basics/SKILL.md
others/skills/adaptations/population-genetics-plink-basics/UPSTREAM.md
others/skills/adaptations/population-genetics-population-structure/DNAKIT.md
others/skills/adaptations/population-genetics-population-structure/SKILL.md
others/skills/adaptations/population-genetics-population-structure/UPSTREAM.md
others/skills/adaptations/population-genetics-rare-variant-association/DNAKIT.md
others/skills/adaptations/population-genetics-rare-variant-association/SKILL.md
others/skills/adaptations/population-genetics-rare-variant-association/UPSTREAM.md
others/skills/adaptations/population-genetics-scikit-allel-analysis/DNAKIT.md
others/skills/adaptations/population-genetics-scikit-allel-analysis/SKILL.md
others/skills/adaptations/population-genetics-scikit-allel-analysis/UPSTREAM.md
others/skills/adaptations/population-genetics-selection-statistics/DNAKIT.md
others/skills/adaptations/population-genetics-selection-statistics/SKILL.md
others/skills/adaptations/population-genetics-selection-statistics/UPSTREAM.md
others/skills/adaptations/prefect-dask-nextflow/DNAKIT.md
others/skills/adaptations/prefect-dask-nextflow/SKILL.md
others/skills/adaptations/prefect-dask-nextflow/UPSTREAM.md
others/skills/adaptations/prepare-rare-disease-case/DNAKIT.md
others/skills/adaptations/prepare-rare-disease-case/SKILL.md
others/skills/adaptations/prepare-rare-disease-case/UPSTREAM.md
others/skills/adaptations/primer-design-primer-basics/DNAKIT.md
others/skills/adaptations/primer-design-primer-basics/SKILL.md
others/skills/adaptations/primer-design-primer-basics/UPSTREAM.md
others/skills/adaptations/primer-design-primer-specificity/DNAKIT.md
others/skills/adaptations/primer-design-primer-specificity/SKILL.md
others/skills/adaptations/primer-design-primer-specificity/UPSTREAM.md
others/skills/adaptations/primer-design-primer-validation/DNAKIT.md
others/skills/adaptations/primer-design-primer-validation/SKILL.md
others/skills/adaptations/primer-design-primer-validation/UPSTREAM.md
others/skills/adaptations/primer-design-qpcr-primers/DNAKIT.md
others/skills/adaptations/primer-design-qpcr-primers/SKILL.md
others/skills/adaptations/primer-design-qpcr-primers/UPSTREAM.md
others/skills/adaptations/progenomes/DNAKIT.md
others/skills/adaptations/progenomes/SKILL.md
others/skills/adaptations/progenomes/UPSTREAM.md
others/skills/adaptations/protein-lof-mechanism/DNAKIT.md
others/skills/adaptations/protein-lof-mechanism/SKILL.md
others/skills/adaptations/protein-lof-mechanism/UPSTREAM.md
others/skills/adaptations/protein-sae-variant-interpretation/DNAKIT.md
others/skills/adaptations/protein-sae-variant-interpretation/SKILL.md
others/skills/adaptations/protein-sae-variant-interpretation/UPSTREAM.md
others/skills/adaptations/pysam/DNAKIT.md
others/skills/adaptations/pysam/SKILL.md
others/skills/adaptations/pysam/UPSTREAM.md
others/skills/adaptations/qsap/DNAKIT.md
others/skills/adaptations/qsap/SKILL.md
others/skills/adaptations/qsap/UPSTREAM.md
others/skills/adaptations/quality-assessment/DNAKIT.md
others/skills/adaptations/quality-assessment/SKILL.md
others/skills/adaptations/quality-assessment/UPSTREAM.md
others/skills/adaptations/quality-assessment/references/literature.md
others/skills/adaptations/rare-disease-diagnosis/DIAGNOSTIC_WORKFLOW.md
others/skills/adaptations/rare-disease-diagnosis/DNAKIT.md
others/skills/adaptations/rare-disease-diagnosis/SKILL.md
others/skills/adaptations/rare-disease-diagnosis/TOOLS_REFERENCE.md
others/skills/adaptations/rare-disease-diagnosis/UPSTREAM.md
others/skills/adaptations/rare-disease-genomics/DNAKIT.md
others/skills/adaptations/rare-disease-genomics/SKILL.md
others/skills/adaptations/rare-disease-genomics/UPSTREAM.md
others/skills/adaptations/rare-high-impact-variants/DNAKIT.md
others/skills/adaptations/rare-high-impact-variants/SKILL.md
others/skills/adaptations/rare-high-impact-variants/UPSTREAM.md
others/skills/adaptations/read-alignment-bowtie2-alignment/DNAKIT.md
others/skills/adaptations/read-alignment-bowtie2-alignment/SKILL.md
others/skills/adaptations/read-alignment-bowtie2-alignment/UPSTREAM.md
others/skills/adaptations/read-alignment-bwa-alignment/DNAKIT.md
others/skills/adaptations/read-alignment-bwa-alignment/SKILL.md
others/skills/adaptations/read-alignment-bwa-alignment/UPSTREAM.md
others/skills/adaptations/read-qc-adapter-trimming/DNAKIT.md
others/skills/adaptations/read-qc-adapter-trimming/SKILL.md
others/skills/adaptations/read-qc-adapter-trimming/UPSTREAM.md
others/skills/adaptations/read-qc-contamination-screening/DNAKIT.md
others/skills/adaptations/read-qc-contamination-screening/SKILL.md
others/skills/adaptations/read-qc-contamination-screening/UPSTREAM.md
others/skills/adaptations/read-qc-fastp-workflow/DNAKIT.md
others/skills/adaptations/read-qc-fastp-workflow/SKILL.md
others/skills/adaptations/read-qc-fastp-workflow/UPSTREAM.md
others/skills/adaptations/read-qc-quality-filtering/DNAKIT.md
others/skills/adaptations/read-qc-quality-filtering/SKILL.md
others/skills/adaptations/read-qc-quality-filtering/UPSTREAM.md
others/skills/adaptations/read-qc-quality-reports/DNAKIT.md
others/skills/adaptations/read-qc-quality-reports/SKILL.md
others/skills/adaptations/read-qc-quality-reports/UPSTREAM.md
others/skills/adaptations/read-qc-umi-processing/DNAKIT.md
others/skills/adaptations/read-qc-umi-processing/SKILL.md
others/skills/adaptations/read-qc-umi-processing/UPSTREAM.md
others/skills/adaptations/read-sequences/DNAKIT.md
others/skills/adaptations/read-sequences/SKILL.md
others/skills/adaptations/read-sequences/UPSTREAM.md
others/skills/adaptations/recombinator/DNAKIT.md
others/skills/adaptations/recombinator/SKILL.md
others/skills/adaptations/recombinator/UPSTREAM.md
others/skills/adaptations/recombinator/recombinator.py
others/skills/adaptations/reference-operations/DNAKIT.md
others/skills/adaptations/reference-operations/SKILL.md
others/skills/adaptations/reference-operations/UPSTREAM.md
others/skills/adaptations/regulatory-elements/DNAKIT.md
others/skills/adaptations/regulatory-elements/SKILL.md
others/skills/adaptations/regulatory-elements/UPSTREAM.md
others/skills/adaptations/regulatory-elements/references/literature.md
others/skills/adaptations/regulatory-genomics/DNAKIT.md
others/skills/adaptations/regulatory-genomics/SKILL.md
others/skills/adaptations/regulatory-genomics/UPSTREAM.md
others/skills/adaptations/regulatory-variant-analysis/DNAKIT.md
others/skills/adaptations/regulatory-variant-analysis/SKILL.md
others/skills/adaptations/regulatory-variant-analysis/UPSTREAM.md
others/skills/adaptations/regulomedb-database/DNAKIT.md
others/skills/adaptations/regulomedb-database/SKILL.md
others/skills/adaptations/regulomedb-database/UPSTREAM.md
others/skills/adaptations/remap-database/DNAKIT.md
others/skills/adaptations/remap-database/SKILL.md
others/skills/adaptations/remap-database/UPSTREAM.md
others/skills/adaptations/restriction-enzyme-selection/DNAKIT.md
others/skills/adaptations/restriction-enzyme-selection/SKILL.md
others/skills/adaptations/restriction-enzyme-selection/UPSTREAM.md
others/skills/adaptations/restriction-fragment-analysis/DNAKIT.md
others/skills/adaptations/restriction-fragment-analysis/SKILL.md
others/skills/adaptations/restriction-fragment-analysis/UPSTREAM.md
others/skills/adaptations/restriction-golden-gate-assembly/DNAKIT.md
others/skills/adaptations/restriction-golden-gate-assembly/SKILL.md
others/skills/adaptations/restriction-golden-gate-assembly/UPSTREAM.md
others/skills/adaptations/restriction-mapping/DNAKIT.md
others/skills/adaptations/restriction-mapping/SKILL.md
others/skills/adaptations/restriction-mapping/UPSTREAM.md
others/skills/adaptations/restriction-sites/DNAKIT.md
others/skills/adaptations/restriction-sites/SKILL.md
others/skills/adaptations/restriction-sites/UPSTREAM.md
others/skills/adaptations/reverse-complement/DNAKIT.md
others/skills/adaptations/reverse-complement/SKILL.md
others/skills/adaptations/reverse-complement/UPSTREAM.md
others/skills/adaptations/review-variant-table/DNAKIT.md
others/skills/adaptations/review-variant-table/SKILL.md
others/skills/adaptations/review-variant-table/UPSTREAM.md
others/skills/adaptations/sam-bam-basics/DNAKIT.md
others/skills/adaptations/sam-bam-basics/SKILL.md
others/skills/adaptations/sam-bam-basics/UPSTREAM.md
others/skills/adaptations/sample-qc-triage/DNAKIT.md
others/skills/adaptations/sample-qc-triage/SKILL.md
others/skills/adaptations/sample-qc-triage/UPSTREAM.md
others/skills/adaptations/samtools-bam-processing/DNAKIT.md
others/skills/adaptations/samtools-bam-processing/SKILL.md
others/skills/adaptations/samtools-bam-processing/UPSTREAM.md
others/skills/adaptations/scikit-bio/DNAKIT.md
others/skills/adaptations/scikit-bio/SKILL.md
others/skills/adaptations/scikit-bio/UPSTREAM.md
others/skills/adaptations/seq-objects/DNAKIT.md
others/skills/adaptations/seq-objects/SKILL.md
others/skills/adaptations/seq-objects/UPSTREAM.md
others/skills/adaptations/seq-wrangler/DNAKIT.md
others/skills/adaptations/seq-wrangler/README.md
others/skills/adaptations/seq-wrangler/SKILL.md
others/skills/adaptations/seq-wrangler/UPSTREAM.md
others/skills/adaptations/sequence-analysis/DNAKIT.md
others/skills/adaptations/sequence-analysis/SKILL.md
others/skills/adaptations/sequence-analysis/UPSTREAM.md
others/skills/adaptations/sequence-properties/DNAKIT.md
others/skills/adaptations/sequence-properties/SKILL.md
others/skills/adaptations/sequence-properties/UPSTREAM.md
others/skills/adaptations/sequence-retrieval/CHECKLIST.md
others/skills/adaptations/sequence-retrieval/DNAKIT.md
others/skills/adaptations/sequence-retrieval/SKILL.md
others/skills/adaptations/sequence-retrieval/UPSTREAM.md
others/skills/adaptations/sequence-retrieval/examples.md
others/skills/adaptations/sequence-slicing/DNAKIT.md
others/skills/adaptations/sequence-slicing/SKILL.md
others/skills/adaptations/sequence-slicing/UPSTREAM.md
others/skills/adaptations/sequence-statistics/DNAKIT.md
others/skills/adaptations/sequence-statistics/SKILL.md
others/skills/adaptations/sequence-statistics/UPSTREAM.md
others/skills/adaptations/single-cell-clustering/DNAKIT.md
others/skills/adaptations/single-cell-clustering/SKILL.md
others/skills/adaptations/single-cell-clustering/UPSTREAM.md
others/skills/adaptations/single-cell-data-io/DNAKIT.md
others/skills/adaptations/single-cell-data-io/SKILL.md
others/skills/adaptations/single-cell-data-io/UPSTREAM.md
others/skills/adaptations/single-cell-lineage-tracing/DNAKIT.md
others/skills/adaptations/single-cell-lineage-tracing/SKILL.md
others/skills/adaptations/single-cell-lineage-tracing/UPSTREAM.md
others/skills/adaptations/single-cell-multimodal-integration/DNAKIT.md
others/skills/adaptations/single-cell-multimodal-integration/SKILL.md
others/skills/adaptations/single-cell-multimodal-integration/UPSTREAM.md
others/skills/adaptations/single-cell-preprocessing/DNAKIT.md
others/skills/adaptations/single-cell-preprocessing/SKILL.md
others/skills/adaptations/single-cell-preprocessing/UPSTREAM.md
others/skills/adaptations/singlem/DNAKIT.md
others/skills/adaptations/singlem/SKILL.md
others/skills/adaptations/singlem/UPSTREAM.md
others/skills/adaptations/spacedust/DNAKIT.md
others/skills/adaptations/spacedust/SKILL.md
others/skills/adaptations/spacedust/UPSTREAM.md
others/skills/adaptations/splice-variant-prediction/DNAKIT.md
others/skills/adaptations/splice-variant-prediction/SKILL.md
others/skills/adaptations/splice-variant-prediction/UPSTREAM.md
others/skills/adaptations/sra-data/DNAKIT.md
others/skills/adaptations/sra-data/SKILL.md
others/skills/adaptations/sra-data/UPSTREAM.md
others/skills/adaptations/systems-biology-gene-essentiality/DNAKIT.md
others/skills/adaptations/systems-biology-gene-essentiality/SKILL.md
others/skills/adaptations/systems-biology-gene-essentiality/UPSTREAM.md
others/skills/adaptations/systems-biology-metabolic-reconstruction/DNAKIT.md
others/skills/adaptations/systems-biology-metabolic-reconstruction/SKILL.md
others/skills/adaptations/systems-biology-metabolic-reconstruction/UPSTREAM.md
others/skills/adaptations/taxvamb/DNAKIT.md
others/skills/adaptations/taxvamb/SKILL.md
others/skills/adaptations/taxvamb/UPSTREAM.md
others/skills/adaptations/tcr-bcr-analysis-immcantation-analysis/DNAKIT.md
others/skills/adaptations/tcr-bcr-analysis-immcantation-analysis/SKILL.md
others/skills/adaptations/tcr-bcr-analysis-immcantation-analysis/UPSTREAM.md
others/skills/adaptations/tcr-bcr-analysis-mixcr-analysis/DNAKIT.md
others/skills/adaptations/tcr-bcr-analysis-mixcr-analysis/SKILL.md
others/skills/adaptations/tcr-bcr-analysis-mixcr-analysis/UPSTREAM.md
others/skills/adaptations/tcr-bcr-analysis-repertoire-visualization/DNAKIT.md
others/skills/adaptations/tcr-bcr-analysis-repertoire-visualization/SKILL.md
others/skills/adaptations/tcr-bcr-analysis-repertoire-visualization/UPSTREAM.md
others/skills/adaptations/tcr-bcr-analysis-scirpy-analysis/DNAKIT.md
others/skills/adaptations/tcr-bcr-analysis-scirpy-analysis/SKILL.md
others/skills/adaptations/tcr-bcr-analysis-scirpy-analysis/UPSTREAM.md
others/skills/adaptations/tcr-bcr-analysis-specificity-annotation/DNAKIT.md
others/skills/adaptations/tcr-bcr-analysis-specificity-annotation/SKILL.md
others/skills/adaptations/tcr-bcr-analysis-specificity-annotation/UPSTREAM.md
others/skills/adaptations/tcr-bcr-analysis-vdjtools-analysis/DNAKIT.md
others/skills/adaptations/tcr-bcr-analysis-vdjtools-analysis/SKILL.md
others/skills/adaptations/tcr-bcr-analysis-vdjtools-analysis/UPSTREAM.md
others/skills/adaptations/tiledbvcf/DNAKIT.md
others/skills/adaptations/tiledbvcf/SKILL.md
others/skills/adaptations/tiledbvcf/UPSTREAM.md
others/skills/adaptations/track-experiments/DNAKIT.md
others/skills/adaptations/track-experiments/SKILL.md
others/skills/adaptations/track-experiments/UPSTREAM.md
others/skills/adaptations/track-experiments/references/literature.md
others/skills/adaptations/tracking-taxonomy-updates/DNAKIT.md
others/skills/adaptations/tracking-taxonomy-updates/SKILL.md
others/skills/adaptations/tracking-taxonomy-updates/UPSTREAM.md
others/skills/adaptations/tracking-taxonomy-updates/reference/tools.md
others/skills/adaptations/transcription-translation/DNAKIT.md
others/skills/adaptations/transcription-translation/SKILL.md
others/skills/adaptations/transcription-translation/UPSTREAM.md
others/skills/adaptations/tumor-fraction-estimation/DNAKIT.md
others/skills/adaptations/tumor-fraction-estimation/SKILL.md
others/skills/adaptations/tumor-fraction-estimation/UPSTREAM.md
others/skills/adaptations/ucsc-conservation-and-tfbs/DNAKIT.md
others/skills/adaptations/ucsc-conservation-and-tfbs/SKILL.md
others/skills/adaptations/ucsc-conservation-and-tfbs/UPSTREAM.md
others/skills/adaptations/ucsc-genome-browser/DNAKIT.md
others/skills/adaptations/ucsc-genome-browser/SKILL.md
others/skills/adaptations/ucsc-genome-browser/UPSTREAM.md
others/skills/adaptations/unibind-database/DNAKIT.md
others/skills/adaptations/unibind-database/SKILL.md
others/skills/adaptations/unibind-database/UPSTREAM.md
others/skills/adaptations/unicore/DNAKIT.md
others/skills/adaptations/unicore/SKILL.md
others/skills/adaptations/unicore/UPSTREAM.md
others/skills/adaptations/variant-analysis/DNAKIT.md
others/skills/adaptations/variant-analysis/QUICK_START.md
others/skills/adaptations/variant-analysis/SKILL.md
others/skills/adaptations/variant-analysis/UPSTREAM.md
others/skills/adaptations/variant-analysis/python_implementation.py
others/skills/adaptations/variant-analysis/test_variant_analysis.py
others/skills/adaptations/variant-analysis/references/annotation_guide.md
others/skills/adaptations/variant-analysis/references/sv_cnv_analysis.md
others/skills/adaptations/variant-analysis/scripts/annotate_variants.py
others/skills/adaptations/variant-annotation/DNAKIT.md
others/skills/adaptations/variant-annotation/SKILL.md
others/skills/adaptations/variant-annotation/UPSTREAM.md
others/skills/adaptations/variant-calling/DNAKIT.md
others/skills/adaptations/variant-calling/SKILL.md
others/skills/adaptations/variant-calling/UPSTREAM.md
others/skills/adaptations/variant-calling-deepvariant/DNAKIT.md
others/skills/adaptations/variant-calling-deepvariant/SKILL.md
others/skills/adaptations/variant-calling-deepvariant/UPSTREAM.md
others/skills/adaptations/variant-calling-filtering-best-practices/DNAKIT.md
others/skills/adaptations/variant-calling-filtering-best-practices/SKILL.md
others/skills/adaptations/variant-calling-filtering-best-practices/UPSTREAM.md
others/skills/adaptations/variant-calling-joint-calling/DNAKIT.md
others/skills/adaptations/variant-calling-joint-calling/SKILL.md
others/skills/adaptations/variant-calling-joint-calling/UPSTREAM.md
others/skills/adaptations/variant-calling-structural-variant-calling/DNAKIT.md
others/skills/adaptations/variant-calling-structural-variant-calling/SKILL.md
others/skills/adaptations/variant-calling-structural-variant-calling/UPSTREAM.md
others/skills/adaptations/variant-interpretation/CODE_PATTERNS.md
others/skills/adaptations/variant-interpretation/DNAKIT.md
others/skills/adaptations/variant-interpretation/SKILL.md
others/skills/adaptations/variant-interpretation/TOOLS_REFERENCE.md
others/skills/adaptations/variant-interpretation/UPSTREAM.md
others/skills/adaptations/variant-normalization/DNAKIT.md
others/skills/adaptations/variant-normalization/SKILL.md
others/skills/adaptations/variant-normalization/UPSTREAM.md
others/skills/adaptations/variant-predictor-dms-validation/DNAKIT.md
others/skills/adaptations/variant-predictor-dms-validation/SKILL.md
others/skills/adaptations/variant-predictor-dms-validation/UPSTREAM.md
others/skills/adaptations/variant-to-mechanism/DNAKIT.md
others/skills/adaptations/variant-to-mechanism/SKILL.md
others/skills/adaptations/variant-to-mechanism/UPSTREAM.md
others/skills/adaptations/vcf-basics/DNAKIT.md
others/skills/adaptations/vcf-basics/SKILL.md
others/skills/adaptations/vcf-basics/UPSTREAM.md
others/skills/adaptations/vcf-manipulation/DNAKIT.md
others/skills/adaptations/vcf-manipulation/SKILL.md
others/skills/adaptations/vcf-manipulation/UPSTREAM.md
others/skills/adaptations/vcf-statistics/DNAKIT.md
others/skills/adaptations/vcf-statistics/SKILL.md
others/skills/adaptations/vcf-statistics/UPSTREAM.md
others/skills/adaptations/vcontact/DNAKIT.md
others/skills/adaptations/vcontact/SKILL.md
others/skills/adaptations/vcontact/UPSTREAM.md
others/skills/adaptations/viromics/DNAKIT.md
others/skills/adaptations/viromics/SKILL.md
others/skills/adaptations/viromics/UPSTREAM.md
others/skills/adaptations/viromics/docs/README.md
others/skills/adaptations/viromics/docs/genomad-usage.md
others/skills/adaptations/viromics/scripts/build_viromics_evidence.py
others/skills/adaptations/virulencefinder/DNAKIT.md
others/skills/adaptations/virulencefinder/SKILL.md
others/skills/adaptations/virulencefinder/UPSTREAM.md
others/skills/adaptations/vitis-pangenome/DNAKIT.md
others/skills/adaptations/vitis-pangenome/SKILL.md
others/skills/adaptations/vitis-pangenome/UPSTREAM.md
others/skills/adaptations/vitis-popgen/DNAKIT.md
others/skills/adaptations/vitis-popgen/SKILL.md
others/skills/adaptations/vitis-popgen/UPSTREAM.md
others/skills/adaptations/vitis-te/DNAKIT.md
others/skills/adaptations/vitis-te/SKILL.md
others/skills/adaptations/vitis-te/UPSTREAM.md
others/skills/adaptations/wgs-prs/DNAKIT.md
others/skills/adaptations/wgs-prs/SKILL.md
others/skills/adaptations/wgs-prs/UPSTREAM.md
others/skills/adaptations/wgs-prs/repro_bundle.py
others/skills/adaptations/wgs-prs/wgs_prs.py
others/skills/adaptations/wgs-prs/tests/test_repro_bundle.py
others/skills/adaptations/wgs-prs/tests/test_sarek.py
others/skills/adaptations/wgs-prs/tests/test_vcf_qc.py
others/skills/adaptations/wgs-prs/tests/test_wgs_prs.py
others/skills/adaptations/workflow-management-cwl-workflows/DNAKIT.md
others/skills/adaptations/workflow-management-cwl-workflows/SKILL.md
others/skills/adaptations/workflow-management-cwl-workflows/UPSTREAM.md
others/skills/adaptations/workflow-management-nextflow-pipelines/DNAKIT.md
others/skills/adaptations/workflow-management-nextflow-pipelines/SKILL.md
others/skills/adaptations/workflow-management-nextflow-pipelines/UPSTREAM.md
others/skills/adaptations/workflow-management-nf-core-pipelines/DNAKIT.md
others/skills/adaptations/workflow-management-nf-core-pipelines/SKILL.md
others/skills/adaptations/workflow-management-nf-core-pipelines/UPSTREAM.md
others/skills/adaptations/workflow-management-snakemake-workflows/DNAKIT.md
others/skills/adaptations/workflow-management-snakemake-workflows/SKILL.md
others/skills/adaptations/workflow-management-snakemake-workflows/UPSTREAM.md
others/skills/adaptations/workflow-management-wdl-workflows/DNAKIT.md
others/skills/adaptations/workflow-management-wdl-workflows/SKILL.md
others/skills/adaptations/workflow-management-wdl-workflows/UPSTREAM.md
others/skills/adaptations/workflow-methods-docwriter/DNAKIT.md
others/skills/adaptations/workflow-methods-docwriter/SKILL.md
others/skills/adaptations/workflow-methods-docwriter/UPSTREAM.md
others/skills/adaptations/workflows-atacseq-pipeline/DNAKIT.md
others/skills/adaptations/workflows-atacseq-pipeline/SKILL.md
others/skills/adaptations/workflows-atacseq-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-causal-genomics-pipeline/DNAKIT.md
others/skills/adaptations/workflows-causal-genomics-pipeline/SKILL.md
others/skills/adaptations/workflows-causal-genomics-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-chipseq-pipeline/DNAKIT.md
others/skills/adaptations/workflows-chipseq-pipeline/SKILL.md
others/skills/adaptations/workflows-chipseq-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-cnv-pipeline/DNAKIT.md
others/skills/adaptations/workflows-cnv-pipeline/SKILL.md
others/skills/adaptations/workflows-cnv-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-crispr-editing-pipeline/DNAKIT.md
others/skills/adaptations/workflows-crispr-editing-pipeline/SKILL.md
others/skills/adaptations/workflows-crispr-editing-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-crispr-screen-pipeline/DNAKIT.md
others/skills/adaptations/workflows-crispr-screen-pipeline/SKILL.md
others/skills/adaptations/workflows-crispr-screen-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-edna-pipeline/DNAKIT.md
others/skills/adaptations/workflows-edna-pipeline/SKILL.md
others/skills/adaptations/workflows-edna-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-fastq-to-variants/DNAKIT.md
others/skills/adaptations/workflows-fastq-to-variants/SKILL.md
others/skills/adaptations/workflows-fastq-to-variants/UPSTREAM.md
others/skills/adaptations/workflows-genome-annotation-pipeline/DNAKIT.md
others/skills/adaptations/workflows-genome-annotation-pipeline/SKILL.md
others/skills/adaptations/workflows-genome-annotation-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-genome-assembly-pipeline/DNAKIT.md
others/skills/adaptations/workflows-genome-assembly-pipeline/SKILL.md
others/skills/adaptations/workflows-genome-assembly-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-gwas-pipeline/DNAKIT.md
others/skills/adaptations/workflows-gwas-pipeline/SKILL.md
others/skills/adaptations/workflows-gwas-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-hic-pipeline/DNAKIT.md
others/skills/adaptations/workflows-hic-pipeline/SKILL.md
others/skills/adaptations/workflows-hic-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-liquid-biopsy-pipeline/DNAKIT.md
others/skills/adaptations/workflows-liquid-biopsy-pipeline/SKILL.md
others/skills/adaptations/workflows-liquid-biopsy-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-longread-sv-pipeline/DNAKIT.md
others/skills/adaptations/workflows-longread-sv-pipeline/SKILL.md
others/skills/adaptations/workflows-longread-sv-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-metagenomics-pipeline/DNAKIT.md
others/skills/adaptations/workflows-metagenomics-pipeline/SKILL.md
others/skills/adaptations/workflows-metagenomics-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-methylation-pipeline/DNAKIT.md
others/skills/adaptations/workflows-methylation-pipeline/SKILL.md
others/skills/adaptations/workflows-methylation-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-microbiome-pipeline/DNAKIT.md
others/skills/adaptations/workflows-microbiome-pipeline/SKILL.md
others/skills/adaptations/workflows-microbiome-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-multiome-pipeline/DNAKIT.md
others/skills/adaptations/workflows-multiome-pipeline/SKILL.md
others/skills/adaptations/workflows-multiome-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-neoantigen-pipeline/DNAKIT.md
others/skills/adaptations/workflows-neoantigen-pipeline/SKILL.md
others/skills/adaptations/workflows-neoantigen-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-outbreak-pipeline/DNAKIT.md
others/skills/adaptations/workflows-outbreak-pipeline/SKILL.md
others/skills/adaptations/workflows-outbreak-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-somatic-variant-pipeline/DNAKIT.md
others/skills/adaptations/workflows-somatic-variant-pipeline/SKILL.md
others/skills/adaptations/workflows-somatic-variant-pipeline/UPSTREAM.md
others/skills/adaptations/workflows-tcr-pipeline/DNAKIT.md
others/skills/adaptations/workflows-tcr-pipeline/SKILL.md
others/skills/adaptations/workflows-tcr-pipeline/UPSTREAM.md
others/skills/adaptations/write-sequences/DNAKIT.md
others/skills/adaptations/write-sequences/SKILL.md
others/skills/adaptations/write-sequences/UPSTREAM.md
others/tests/test_cli_workflows.py
others/tests/test_import.py
others/tests/test_static_demo.py
others/tests/boundary/conftest.py
others/tests/boundary/test_f_downloads.py
others/tests/boundary/test_f_prediction.py
others/tests/boundary/test_f_processing.py
others/tests/boundary/test_f_visualization.py
others/tests/integration/test_downloaded_dna_structures.py
others/tests/unit/test_agent_development.py
others/tests/unit/test_agent_development_resume.py
others/tests/unit/test_agent_execution.py
others/tests/unit/test_agent_knowledge.py
others/tests/unit/test_agent_repair.py
others/tests/unit/test_agent_resume.py
others/tests/unit/test_agent_runner.py
others/tests/unit/test_agent_tools.py
others/tests/unit/test_alignment_pairwise.py
others/tests/unit/test_backends_registry.py
others/tests/unit/test_batch.py
others/tests/unit/test_bioinformatics_external.py
others/tests/unit/test_bioinformatics_io_workflows.py
others/tests/unit/test_bioinformatics_native.py
others/tests/unit/test_cache_store.py
others/tests/unit/test_chunking.py
others/tests/unit/test_chunking_paired.py
others/tests/unit/test_config_loader.py
others/tests/unit/test_core_coordinates.py
others/tests/unit/test_core_facade.py
others/tests/unit/test_core_records.py
others/tests/unit/test_core_results.py
others/tests/unit/test_core_sequence.py
others/tests/unit/test_custom_alphagenome_training.py
others/tests/unit/test_custom_enformer_training.py
others/tests/unit/test_custom_native_training.py
others/tests/unit/test_custom_property_training.py
others/tests/unit/test_custom_training_scheduler.py
others/tests/unit/test_custom_transformers_training.py
others/tests/unit/test_datasets_advanced_deduplicate.py
others/tests/unit/test_datasets_advanced_split_evaluation.py
others/tests/unit/test_datasets_clustering.py
others/tests/unit/test_datasets_deduplicate.py
others/tests/unit/test_datasets_filter.py
others/tests/unit/test_datasets_kfold.py
others/tests/unit/test_datasets_sampling.py
others/tests/unit/test_datasets_split.py
others/tests/unit/test_datasets_tabular.py
others/tests/unit/test_descriptors_all.py
others/tests/unit/test_descriptors_basic.py
others/tests/unit/test_descriptors_complexity.py
others/tests/unit/test_descriptors_kmer_entropy.py
others/tests/unit/test_descriptors_runs_windows_codons.py
others/tests/unit/test_development_quality.py
others/tests/unit/test_development_transactions.py
others/tests/unit/test_evaluation_batch_contract.py
others/tests/unit/test_evaluation_collection.py
others/tests/unit/test_evaluation_collection_plot_output.py
others/tests/unit/test_evaluation_distribution_risk_scorecard.py
others/tests/unit/test_evaluation_frechet.py
others/tests/unit/test_evaluation_generative.py
others/tests/unit/test_evaluation_novelty_plot_output.py
others/tests/unit/test_evaluation_reference.py
others/tests/unit/test_evaluation_reference_consistency.py
others/tests/unit/test_evaluation_sequence.py
others/tests/unit/test_external_backend_adapters.py
others/tests/unit/test_fasta_direction_parallel.py
others/tests/unit/test_fingerprints_advanced.py
others/tests/unit/test_fingerprints_bit.py
others/tests/unit/test_fingerprints_encoding.py
others/tests/unit/test_fingerprints_kmer.py
others/tests/unit/test_fingerprints_sketch.py
others/tests/unit/test_gene_annotation.py
others/tests/unit/test_genomics_ani.py
others/tests/unit/test_genomics_breeding.py
others/tests/unit/test_genomics_external_mcp.py
others/tests/unit/test_genomics_genes.py
others/tests/unit/test_genomics_integrations.py
others/tests/unit/test_genomics_methylation.py
others/tests/unit/test_genomics_nanotechnology.py
others/tests/unit/test_genomics_population.py
others/tests/unit/test_genomics_skill_expansion.py
others/tests/unit/test_genomics_storage.py
others/tests/unit/test_io_annotations_advanced.py
others/tests/unit/test_io_config_results.py
others/tests/unit/test_io_genbank_advanced.py
others/tests/unit/test_io_indexed_advanced.py
others/tests/unit/test_io_metadata_advanced.py
others/tests/unit/test_io_rows_artifacts.py
others/tests/unit/test_io_sequence_formats.py
others/tests/unit/test_io_source.py
others/tests/unit/test_io_structured.py
others/tests/unit/test_io_tables_advanced.py
others/tests/unit/test_llm.py
others/tests/unit/test_llm_files.py
others/tests/unit/test_llm_providers.py
others/tests/unit/test_machine_learning_properties.py
others/tests/unit/test_molbio_optimization.py
others/tests/unit/test_molbio_primers_crispr.py
others/tests/unit/test_molbio_restriction_assembly.py
others/tests/unit/test_native_skill_functions.py
others/tests/unit/test_native_workflow_execution.py
others/tests/unit/test_neural_clustering.py
others/tests/unit/test_ops_circular.py
others/tests/unit/test_ops_direction_files.py
others/tests/unit/test_ops_direction_translation.py
others/tests/unit/test_ops_edit.py
others/tests/unit/test_ops_evolution.py
others/tests/unit/test_ops_mutation_concat.py
others/tests/unit/test_ops_records.py
others/tests/unit/test_patterns_coding_restriction_crispr.py
others/tests/unit/test_patterns_motif.py
others/tests/unit/test_patterns_regions_repeats.py
others/tests/unit/test_prediction_checkpoint_downloads.py
others/tests/unit/test_prediction_dependency_hints.py
others/tests/unit/test_processing_inputs.py
others/tests/unit/test_processing_parallel.py
others/tests/unit/test_processing_regions.py
others/tests/unit/test_progress_time.py
others/tests/unit/test_property_prediction.py
others/tests/unit/test_references.py
others/tests/unit/test_release_archives.py
others/tests/unit/test_remote_download.py
others/tests/unit/test_remote_search.py
others/tests/unit/test_runtime_updates.py
others/tests/unit/test_schema_llm_providers.py
others/tests/unit/test_scientific_functions.py
others/tests/unit/test_secondary_structure.py
others/tests/unit/test_sequence_retrieval.py
others/tests/unit/test_similarity_approximate.py
others/tests/unit/test_similarity_dashing.py
others/tests/unit/test_similarity_distance.py
others/tests/unit/test_similarity_index.py
others/tests/unit/test_similarity_search.py
others/tests/unit/test_similarity_sketch.py
others/tests/unit/test_similarity_vector_matrix.py
others/tests/unit/test_skill_adaptations.py
others/tests/unit/test_skills.py
others/tests/unit/test_split_progress.py
others/tests/unit/test_standardize_gaps.py
others/tests/unit/test_standardize_normalize.py
others/tests/unit/test_standardize_validate.py
others/tests/unit/test_structure3d.py
others/tests/unit/test_thermodynamics_backends.py
others/tests/unit/test_thermodynamics_calculations.py
others/tests/unit/test_thermodynamics_optics_equilibrium.py
others/tests/unit/test_tool_compatibility.py
others/tests/unit/test_tool_contributions.py
others/tests/unit/test_tool_development_packaging.py
others/tests/unit/test_tool_embedding_search.py
others/tests/unit/test_tool_generation.py
others/tests/unit/test_tool_optimization.py
others/tests/unit/test_tool_repair.py
others/tests/unit/test_user_catalog_analyses.py
others/tests/unit/test_user_catalog_analysis_backends.py
others/tests/unit/test_user_catalog_import.py
others/tests/unit/test_user_catalog_skills.py
others/tests/unit/test_verbosity.py
others/tests/unit/test_visualization_advanced.py
others/tests/unit/test_visualization_charts.py
others/tests/unit/test_visualization_confusion.py
others/tests/unit/test_visualization_distribution.py
others/tests/unit/test_visualization_embedding_errors.py
others/tests/unit/test_visualization_export.py
others/tests/unit/test_visualization_learning.py
others/tests/unit/test_visualization_metric.py
others/tests/unit/test_visualization_sequence.py
others/tests/unit/test_web_search.py
others/tests/unit/test_workflow_cli.py
others/tests/unit/test_workflow_manifest.py
others/tests/unit/test_workflow_runner.py
others/tests/validation/test_validation_runner.py
others/validation/CODE_REVIEW.md
others/validation/README.md
others/validation/STRUCTURE_FEATURE_CODE_REVIEW.md
others/validation/__init__.py
others/validation/audit_table1.py
others/validation/genomics_backends.py
others/validation/pip_genomics.py
others/validation/release_archives.py
others/validation/run_validation.py
others/validation/sync_paper_features.py
others/validation/fixtures/README.md
others/validation/results/local_validation_report.json
registry/README.md
registry/adaptations.json
registry/catalog.json
registry/decisions.json
registry/discovery.json
registry/discovery.md
registry/expansion.json
registry/genomics-backend-validation.json
registry/genomics-expansion-validation.json
registry/genomics-native-skills.json
registry/genomics-new-skills.json
registry/genomics-skills-review.json
registry/genomics-survey.json
registry/migration-validation.json
registry/migration.json
registry/native-api-documentation-validation.json
registry/native-api-documentation.json
registry/native-extensions.json
registry/native-providers.json
registry/pip-genomics-validation.json
registry/provider-effects.json
registry/skill-names.json
registry/skills.csv
registry/sources.json
registry/user-catalog-335.json
registry/user-catalog-analysis-review.json
registry/user-catalog-context-review.json
registry/user-catalog-evidence.json
registry/user-catalog-mcp-review.json
registry/user-catalog-skill-selection.json
registry/user-catalog-skills-review.json
registry/user-catalog-skills.json
registry/user-catalog-validation.json
registry/validation.json
registry/genomics-survey-parts/breeding.json
registry/genomics-survey-parts/clinical.json
registry/genomics-survey-parts/crossdomain.json
registry/genomics-survey-parts/regulation.json
skills/LICENSE.ToolUniverse
skills/README.md
skills/upstream-manifest.json
skills/accessibility-aggregation/DNAKIT.md
skills/accessibility-aggregation/SKILL.md
skills/accessibility-aggregation/UPSTREAM.md
skills/accessibility-aggregation/licenses/encode-toolkit/CITATION.cff
skills/accessibility-aggregation/licenses/encode-toolkit/LICENSE
skills/accessibility-aggregation/references/atac-vs-dnase.md
skills/accessibility-aggregation/references/literature.md
skills/accessibility-aggregation/scripts/validate_peaks.py
skills/alignment-amplicon-clipping/DNAKIT.md
skills/alignment-amplicon-clipping/SKILL.md
skills/alignment-amplicon-clipping/UPSTREAM.md
skills/alignment-amplicon-clipping/usage-guide.md
skills/alignment-amplicon-clipping/examples/ampliconclip_workflow.sh
skills/alignment-amplicon-clipping/licenses/bioskills/LICENSE
skills/alignment-filtering/DNAKIT.md
skills/alignment-filtering/SKILL.md
skills/alignment-filtering/UPSTREAM.md
skills/alignment-filtering/usage-guide.md
skills/alignment-filtering/examples/filter_bam.py
skills/alignment-filtering/licenses/bioskills/LICENSE
skills/alignment-indexing/DNAKIT.md
skills/alignment-indexing/SKILL.md
skills/alignment-indexing/UPSTREAM.md
skills/alignment-indexing/usage-guide.md
skills/alignment-indexing/examples/fetch_regions.py
skills/alignment-indexing/licenses/bioskills/LICENSE
skills/alignment-io/DNAKIT.md
skills/alignment-io/SKILL.md
skills/alignment-io/UPSTREAM.md
skills/alignment-io/usage-guide.md
skills/alignment-io/examples/batch_convert.py
skills/alignment-io/examples/convert_formats.py
skills/alignment-io/examples/read_alignment.py
skills/alignment-io/examples/sample_alignment.aln
skills/alignment-io/examples/slice_alignment.py
skills/alignment-io/licenses/bioskills/LICENSE
skills/alignment-msa-parsing/DNAKIT.md
skills/alignment-msa-parsing/SKILL.md
skills/alignment-msa-parsing/UPSTREAM.md
skills/alignment-msa-parsing/usage-guide.md
skills/alignment-msa-parsing/examples/a2m_a3m_io.py
skills/alignment-msa-parsing/examples/analyze_alignment.py
skills/alignment-msa-parsing/examples/clean_alignment.py
skills/alignment-msa-parsing/examples/consensus_sequence.py
skills/alignment-msa-parsing/examples/find_conserved.py
skills/alignment-msa-parsing/examples/gap_analysis.py
skills/alignment-msa-parsing/examples/henikoff_weights.py
skills/alignment-msa-parsing/examples/mi_apc.py
skills/alignment-msa-parsing/examples/neff.py
skills/alignment-msa-parsing/licenses/bioskills/LICENSE
skills/alignment-msa-statistics/DNAKIT.md
skills/alignment-msa-statistics/SKILL.md
skills/alignment-msa-statistics/UPSTREAM.md
skills/alignment-msa-statistics/usage-guide.md
skills/alignment-msa-statistics/examples/capra_singh_jsd.py
skills/alignment-msa-statistics/examples/conservation_profile.py
skills/alignment-msa-statistics/examples/entropy_analysis.py
skills/alignment-msa-statistics/examples/gap_statistics.py
skills/alignment-msa-statistics/examples/identity_matrix.py
skills/alignment-msa-statistics/examples/kimura_protein_distance.py
skills/alignment-msa-statistics/examples/pssm.py
skills/alignment-msa-statistics/examples/substitution_counts.py
skills/alignment-msa-statistics/licenses/bioskills/LICENSE
skills/alignment-multiple/DNAKIT.md
skills/alignment-multiple/SKILL.md
skills/alignment-multiple/UPSTREAM.md
skills/alignment-multiple/usage-guide.md
skills/alignment-multiple/examples/codon_alignment.py
skills/alignment-multiple/examples/run_msa.py
skills/alignment-multiple/licenses/bioskills/LICENSE
skills/alignment-pairwise/DNAKIT.md
skills/alignment-pairwise/SKILL.md
skills/alignment-pairwise/UPSTREAM.md
skills/alignment-pairwise/usage-guide.md
skills/alignment-pairwise/examples/alignment_from_file.py
skills/alignment-pairwise/examples/empirical_pvalue.py
skills/alignment-pairwise/examples/global_alignment.py
skills/alignment-pairwise/examples/local_alignment.py
skills/alignment-pairwise/examples/protein_alignment.py
skills/alignment-pairwise/licenses/bioskills/LICENSE
skills/alignment-sorting/DNAKIT.md
skills/alignment-sorting/SKILL.md
skills/alignment-sorting/UPSTREAM.md
skills/alignment-sorting/usage-guide.md
skills/alignment-sorting/examples/sort_pipeline.sh
skills/alignment-sorting/licenses/bioskills/LICENSE
skills/alignment-trimming/DNAKIT.md
skills/alignment-trimming/SKILL.md
skills/alignment-trimming/UPSTREAM.md
skills/alignment-trimming/usage-guide.md
skills/alignment-trimming/examples/bmge_trim.py
skills/alignment-trimming/examples/clipkit_trim.py
skills/alignment-trimming/examples/divvier_split.py
skills/alignment-trimming/examples/trimal_modes.py
skills/alignment-trimming/licenses/bioskills/LICENSE
skills/alignment-validation/DNAKIT.md
skills/alignment-validation/SKILL.md
skills/alignment-validation/UPSTREAM.md
skills/alignment-validation/usage-guide.md
skills/alignment-validation/examples/validate_alignment.py
skills/alignment-validation/examples/validate_alignment.sh
skills/alignment-validation/licenses/bioskills/LICENSE
skills/alphagem/DNAKIT.md
skills/alphagem/SKILL.md
skills/alphagem/UPSTREAM.md
skills/alphagem/licenses/pku-metagenomics/LICENSE
skills/alphagem/references/upstream-docs/compute-setup.md
skills/alphagem/references/upstream-docs/getting-started.md
skills/alphagem/references/upstream-docs/multi-platform.md
skills/alphagem/references/upstream-docs/public-databases.md
skills/alphagem/references/upstream-docs/references.md
skills/alphagem/references/upstream-docs/skills.md
skills/alphagem/references/upstream-docs/standard-pipeline.md
skills/alphagem/references/upstream-docs/tool-selection.md
skills/alphagem/references/upstream-docs/troubleshooting.md
skills/alphagenome-atlas-website-links/DNAKIT.md
skills/alphagenome-atlas-website-links/SKILL.md
skills/alphagenome-atlas-website-links/UPSTREAM.md
skills/alphagenome-atlas-website-links/pyproject.toml
skills/alphagenome-atlas-website-links/licenses/deepmind/CC-BY-4.0.txt
skills/alphagenome-atlas-website-links/licenses/deepmind/LICENSE
skills/alphagenome-atlas-website-links/licenses/deepmind/README.md
skills/alphagenome-atlas-website-links/licenses/deepmind/SKILL_LICENSES.md
skills/alphagenome-atlas-website-links/scripts/alphagenome_atlas_links.py
skills/alphagenome-single-variant-analysis/DNAKIT.md
skills/alphagenome-single-variant-analysis/SKILL.md
skills/alphagenome-single-variant-analysis/UPSTREAM.md
skills/alphagenome-single-variant-analysis/pyproject.toml
skills/alphagenome-single-variant-analysis/docs/alphagenome-api.md
skills/alphagenome-single-variant-analysis/docs/interpretation-guide.md
skills/alphagenome-single-variant-analysis/docs/report-templates.md
skills/alphagenome-single-variant-analysis/docs/examples/model_limitation_RNU4ATAC/README.md
skills/alphagenome-single-variant-analysis/docs/examples/model_limitation_RNU4ATAC/ism_skeletal_muscle_RNA_SEQ.png
skills/alphagenome-single-variant-analysis/docs/examples/model_limitation_RNU4ATAC/plot_skeletal_muscle_RNU4ATAC_detail.png
skills/alphagenome-single-variant-analysis/docs/examples/model_limitation_RNU4ATAC/plot_skeletal_muscle_RNU4ATAC_effects.png
skills/alphagenome-single-variant-analysis/docs/examples/model_limitation_RNU4ATAC/plot_skeletal_muscle_RNU4ATAC_wholegene.png
skills/alphagenome-single-variant-analysis/docs/examples/model_limitation_RNU4ATAC/report.md
skills/alphagenome-single-variant-analysis/docs/examples/negative_result_GATA4/README.md
skills/alphagenome-single-variant-analysis/docs/examples/negative_result_GATA4/ism_heart_DNASE.png
skills/alphagenome-single-variant-analysis/docs/examples/negative_result_GATA4/plot_heart_GATA4_detail.png
skills/alphagenome-single-variant-analysis/docs/examples/negative_result_GATA4/plot_heart_GATA4_effects.png
skills/alphagenome-single-variant-analysis/docs/examples/negative_result_GATA4/plot_heart_GATA4_wholegene.png
skills/alphagenome-single-variant-analysis/docs/examples/negative_result_GATA4/report.md
skills/alphagenome-single-variant-analysis/docs/examples/negative_result_TGFB3/README.md
skills/alphagenome-single-variant-analysis/docs/examples/negative_result_TGFB3/ism_heart_ATAC.png
skills/alphagenome-single-variant-analysis/docs/examples/negative_result_TGFB3/ism_heart_RNA_SEQ.png
skills/alphagenome-single-variant-analysis/docs/examples/negative_result_TGFB3/plot_heart_TGFB3_detail.png
skills/alphagenome-single-variant-analysis/docs/examples/negative_result_TGFB3/plot_heart_TGFB3_effects.png
skills/alphagenome-single-variant-analysis/docs/examples/negative_result_TGFB3/plot_heart_TGFB3_wholegene.png
skills/alphagenome-single-variant-analysis/docs/examples/negative_result_TGFB3/report.md
skills/alphagenome-single-variant-analysis/docs/examples/polyadenylation_HBA2/README.md
skills/alphagenome-single-variant-analysis/docs/examples/polyadenylation_HBA2/ism_K562_RNA_SEQ.png
skills/alphagenome-single-variant-analysis/docs/examples/polyadenylation_HBA2/plot_K562_HBA2_effects.png
skills/alphagenome-single-variant-analysis/docs/examples/polyadenylation_HBA2/plot_K562_HBA2_wholegene.png
skills/alphagenome-single-variant-analysis/docs/examples/polyadenylation_HBA2/report.md
skills/alphagenome-single-variant-analysis/docs/examples/regulatory/README.md
skills/alphagenome-single-variant-analysis/docs/examples/regulatory/apoa1_promoter/ism_heart_left_ventricle_RNA_SEQ.png
skills/alphagenome-single-variant-analysis/docs/examples/regulatory/apoa1_promoter/ism_liver_RNA_SEQ.png
skills/alphagenome-single-variant-analysis/docs/examples/regulatory/apoa1_promoter/plot_heart_left_ventricle_APOA1_effects.png
skills/alphagenome-single-variant-analysis/docs/examples/regulatory/apoa1_promoter/plot_liver_APOA1_effects.png
skills/alphagenome-single-variant-analysis/docs/examples/regulatory/apoa1_promoter/report.md
skills/alphagenome-single-variant-analysis/docs/examples/splicing/README.md
skills/alphagenome-single-variant-analysis/docs/examples/splicing/col6a2_exon_extension.png
skills/alphagenome-single-variant-analysis/docs/examples/splicing/col6a2_report.md
skills/alphagenome-single-variant-analysis/docs/examples/splicing/dlg1_exon_skipping.png
skills/alphagenome-single-variant-analysis/docs/examples/splicing/dlg1_report.md
skills/alphagenome-single-variant-analysis/licenses/deepmind/CC-BY-4.0.txt
skills/alphagenome-single-variant-analysis/licenses/deepmind/LICENSE
skills/alphagenome-single-variant-analysis/licenses/deepmind/README.md
skills/alphagenome-single-variant-analysis/licenses/deepmind/SKILL_LICENSES.md
skills/alphagenome-single-variant-analysis/references/citation.bib
skills/alphagenome-single-variant-analysis/scripts/analyze_ism.py
skills/alphagenome-single-variant-analysis/scripts/generate_ontology_mapping.py
skills/alphagenome-single-variant-analysis/scripts/interpret_splicing.py
skills/alphagenome-single-variant-analysis/scripts/lookup_gene_info.py
skills/alphagenome-single-variant-analysis/scripts/resolve_ontology_terms.py
skills/alphagenome-single-variant-analysis/scripts/visualize_genome_tracks.py
skills/alphagenome-single-variant-analysis/scripts/visualize_variant_effects.py
skills/alphagenome-variant-impact-score/DNAKIT.md
skills/alphagenome-variant-impact-score/SKILL.md
skills/alphagenome-variant-impact-score/UPSTREAM.md
skills/alphagenome-variant-impact-score/pyproject.toml
skills/alphagenome-variant-impact-score/licenses/deepmind/CC-BY-4.0.txt
skills/alphagenome-variant-impact-score/licenses/deepmind/LICENSE
skills/alphagenome-variant-impact-score/licenses/deepmind/README.md
skills/alphagenome-variant-impact-score/licenses/deepmind/SKILL_LICENSES.md
skills/alphagenome-variant-impact-score/scripts/alphagenome_atlas_avi.py
skills/amplicon-qc/DNAKIT.md
skills/amplicon-qc/SKILL.md
skills/amplicon-qc/UPSTREAM.md
skills/amplicon-qc/amplicon_qc.R
skills/amplicon-qc/environment.yml
skills/amplicon-qc/licenses/clawbio/CITATION.cff
skills/amplicon-qc/licenses/clawbio/LICENSE
skills/amplicon-qc/tests/preflight_diagnostic.R
skills/amplicon-qc/tests/run_test.sh
skills/amplicon-qc/tests/fixtures/README.md
skills/amplicon-qc/tests/fixtures/demo_R1.fastq.gz
skills/amplicon-qc/tests/fixtures/demo_R2.fastq.gz
skills/analytical-validation/DNAKIT.md
skills/analytical-validation/SKILL.md
skills/analytical-validation/UPSTREAM.md
skills/analytical-validation/usage-guide.md
skills/analytical-validation/examples/detection_limits.py
skills/analytical-validation/licenses/bioskills/LICENSE
skills/analyze-fasta/DNAKIT.md
skills/analyze-fasta/INTENTS.json
skills/analyze-fasta/SKILL.md
skills/analyze-fasta/UPSTREAM.md
skills/analyze-fasta/analyze_fasta.py
skills/analyze-fasta/example_data/demo_nucleotide.fasta
skills/analyze-fasta/example_data/demo_protein.fasta
skills/analyze-fasta/licenses/clawbio/CITATION.cff
skills/analyze-fasta/licenses/clawbio/LICENSE
skills/analyze-fasta/tests/test_analyze_fasta.py
skills/ancestry-risk-profiler/DNAKIT.md
skills/ancestry-risk-profiler/SKILL.md
skills/ancestry-risk-profiler/UPSTREAM.md
skills/ancestry-risk-profiler/ancestry_risk_profiler.py
skills/ancestry-risk-profiler/data/PROVENANCE.md
skills/ancestry-risk-profiler/data/aisnp_panel.csv
skills/ancestry-risk-profiler/data/ancestry_risk_associations.json
skills/ancestry-risk-profiler/data/demo_patient_south_asian.txt
skills/ancestry-risk-profiler/licenses/clawbio/CITATION.cff
skills/ancestry-risk-profiler/licenses/clawbio/LICENSE
skills/ancestry-risk-profiler/tests/test_ancestry_risk_profiler.py
skills/antismash/DNAKIT.md
skills/antismash/SKILL.md
skills/antismash/UPSTREAM.md
skills/antismash/agents/openai.yaml
skills/antismash/licenses/pku-metagenomics/LICENSE
skills/antismash/references/upstream-docs/compute-setup.md
skills/antismash/references/upstream-docs/getting-started.md
skills/antismash/references/upstream-docs/multi-platform.md
skills/antismash/references/upstream-docs/public-databases.md
skills/antismash/references/upstream-docs/references.md
skills/antismash/references/upstream-docs/skills.md
skills/antismash/references/upstream-docs/standard-pipeline.md
skills/antismash/references/upstream-docs/tool-selection.md
skills/antismash/references/upstream-docs/troubleshooting.md
skills/anvio/DNAKIT.md
skills/anvio/SKILL.md
skills/anvio/UPSTREAM.md
skills/anvio/licenses/pku-metagenomics/LICENSE
skills/anvio/references/upstream-docs/compute-setup.md
skills/anvio/references/upstream-docs/getting-started.md
skills/anvio/references/upstream-docs/multi-platform.md
skills/anvio/references/upstream-docs/public-databases.md
skills/anvio/references/upstream-docs/references.md
skills/anvio/references/upstream-docs/skills.md
skills/anvio/references/upstream-docs/standard-pipeline.md
skills/anvio/references/upstream-docs/tool-selection.md
skills/anvio/references/upstream-docs/troubleshooting.md
skills/article-data-fetcher/DNAKIT.md
skills/article-data-fetcher/SKILL.md
skills/article-data-fetcher/UPSTREAM.md
skills/article-data-fetcher/WORKFLOW.md
skills/article-data-fetcher/article_data_fetcher.py
skills/article-data-fetcher/licenses/clawbio/CITATION.cff
skills/article-data-fetcher/licenses/clawbio/LICENSE
skills/article-data-fetcher/tests/test_article_data_fetcher.py
skills/atac-seq-allele-specific-accessibility/DNAKIT.md
skills/atac-seq-allele-specific-accessibility/SKILL.md
skills/atac-seq-allele-specific-accessibility/UPSTREAM.md
skills/atac-seq-allele-specific-accessibility/usage-guide.md
skills/atac-seq-allele-specific-accessibility/examples/wasp_ase_pipeline.sh
skills/atac-seq-allele-specific-accessibility/licenses/bioskills/LICENSE
skills/atac-seq-atac-peak-calling/DNAKIT.md
skills/atac-seq-atac-peak-calling/SKILL.md
skills/atac-seq-atac-peak-calling/UPSTREAM.md
skills/atac-seq-atac-peak-calling/usage-guide.md
skills/atac-seq-atac-peak-calling/examples/call_atac_peaks.sh
skills/atac-seq-atac-peak-calling/licenses/bioskills/LICENSE
skills/atac-seq-atac-qc/DNAKIT.md
skills/atac-seq-atac-qc/SKILL.md
skills/atac-seq-atac-qc/UPSTREAM.md
skills/atac-seq-atac-qc/usage-guide.md
skills/atac-seq-atac-qc/examples/atac_qc_metrics.R
skills/atac-seq-atac-qc/licenses/bioskills/LICENSE
skills/atac-seq-co-accessibility/DNAKIT.md
skills/atac-seq-co-accessibility/SKILL.md
skills/atac-seq-co-accessibility/UPSTREAM.md
skills/atac-seq-co-accessibility/usage-guide.md
skills/atac-seq-co-accessibility/examples/cicero_workflow.R
skills/atac-seq-co-accessibility/licenses/bioskills/LICENSE
skills/atac-seq-consensus-peakset/DNAKIT.md
skills/atac-seq-consensus-peakset/SKILL.md
skills/atac-seq-consensus-peakset/UPSTREAM.md
skills/atac-seq-consensus-peakset/usage-guide.md
skills/atac-seq-consensus-peakset/examples/iterative_overlap.sh
skills/atac-seq-consensus-peakset/licenses/bioskills/LICENSE
skills/atac-seq-deep-learning-atac/DNAKIT.md
skills/atac-seq-deep-learning-atac/SKILL.md
skills/atac-seq-deep-learning-atac/UPSTREAM.md
skills/atac-seq-deep-learning-atac/usage-guide.md
skills/atac-seq-deep-learning-atac/examples/chrombpnet_pipeline.sh
skills/atac-seq-deep-learning-atac/licenses/bioskills/LICENSE
skills/atac-seq-differential-accessibility/DNAKIT.md
skills/atac-seq-differential-accessibility/SKILL.md
skills/atac-seq-differential-accessibility/UPSTREAM.md
skills/atac-seq-differential-accessibility/usage-guide.md
skills/atac-seq-differential-accessibility/examples/diff_accessibility.R
skills/atac-seq-differential-accessibility/licenses/bioskills/LICENSE
skills/atac-seq-enhancer-gene-linking/DNAKIT.md
skills/atac-seq-enhancer-gene-linking/SKILL.md
skills/atac-seq-enhancer-gene-linking/UPSTREAM.md
skills/atac-seq-enhancer-gene-linking/usage-guide.md
skills/atac-seq-enhancer-gene-linking/examples/run_abc.sh
skills/atac-seq-enhancer-gene-linking/licenses/bioskills/LICENSE
skills/atac-seq-footprinting/DNAKIT.md
skills/atac-seq-footprinting/SKILL.md
skills/atac-seq-footprinting/UPSTREAM.md
skills/atac-seq-footprinting/usage-guide.md
skills/atac-seq-footprinting/examples/run_tobias.sh
skills/atac-seq-footprinting/licenses/bioskills/LICENSE
skills/atac-seq-motif-deviation/DNAKIT.md
skills/atac-seq-motif-deviation/SKILL.md
skills/atac-seq-motif-deviation/UPSTREAM.md
skills/atac-seq-motif-deviation/usage-guide.md
skills/atac-seq-motif-deviation/examples/chromvar_analysis.R
skills/atac-seq-motif-deviation/licenses/bioskills/LICENSE
skills/atac-seq-nucleosome-positioning/DNAKIT.md
skills/atac-seq-nucleosome-positioning/SKILL.md
skills/atac-seq-nucleosome-positioning/UPSTREAM.md
skills/atac-seq-nucleosome-positioning/usage-guide.md
skills/atac-seq-nucleosome-positioning/examples/nucleosome_analysis.R
skills/atac-seq-nucleosome-positioning/licenses/bioskills/LICENSE
skills/atac-seq-single-cell-atac/DNAKIT.md
skills/atac-seq-single-cell-atac/SKILL.md
skills/atac-seq-single-cell-atac/UPSTREAM.md
skills/atac-seq-single-cell-atac/usage-guide.md
skills/atac-seq-single-cell-atac/examples/signac_workflow.R
skills/atac-seq-single-cell-atac/licenses/bioskills/LICENSE
skills/bam-statistics/DNAKIT.md
skills/bam-statistics/SKILL.md
skills/bam-statistics/UPSTREAM.md
skills/bam-statistics/usage-guide.md
skills/bam-statistics/examples/qc_report.py
skills/bam-statistics/licenses/bioskills/LICENSE
skills/basalt/DNAKIT.md
skills/basalt/SKILL.md
skills/basalt/UPSTREAM.md
skills/basalt/agents/openai.yaml
skills/basalt/licenses/pku-metagenomics/LICENSE
skills/basalt/references/cli-cheatsheet.md
skills/basalt/references/upstream-docs/compute-setup.md
skills/basalt/references/upstream-docs/getting-started.md
skills/basalt/references/upstream-docs/multi-platform.md
skills/basalt/references/upstream-docs/public-databases.md
skills/basalt/references/upstream-docs/references.md
skills/basalt/references/upstream-docs/skills.md
skills/basalt/references/upstream-docs/standard-pipeline.md
skills/basalt/references/upstream-docs/tool-selection.md
skills/basalt/references/upstream-docs/troubleshooting.md
skills/batch-analysis/DNAKIT.md
skills/batch-analysis/SKILL.md
skills/batch-analysis/UPSTREAM.md
skills/batch-analysis/licenses/encode-toolkit/CITATION.cff
skills/batch-analysis/licenses/encode-toolkit/LICENSE
skills/batch-analysis/references/literature.md
skills/batch-downloads/DNAKIT.md
skills/batch-downloads/SKILL.md
skills/batch-downloads/UPSTREAM.md
skills/batch-downloads/usage-guide.md
skills/batch-downloads/examples/batch_by_ids.py
skills/batch-downloads/examples/batch_fasta.py
skills/batch-downloads/examples/robust_download.py
skills/batch-downloads/licenses/bioskills/LICENSE
skills/batch-processing/DNAKIT.md
skills/batch-processing/SKILL.md
skills/batch-processing/UPSTREAM.md
skills/batch-processing/usage-guide.md
skills/batch-processing/examples/batch_process.py
skills/batch-processing/licenses/bioskills/LICENSE
skills/benchling-integration/DNAKIT.md
skills/benchling-integration/SKILL.md
skills/benchling-integration/UPSTREAM.md
skills/benchling-integration/licenses/kdense/CITATION.cff
skills/benchling-integration/licenses/kdense/LICENSE.md
skills/benchling-integration/licenses/sciagent/CC-BY-4.0.txt
skills/benchling-integration/licenses/sciagent/LICENSE
skills/benchling-integration/licenses/tooluniverse/LICENSE
skills/bigscape/DNAKIT.md
skills/bigscape/SKILL.md
skills/bigscape/UPSTREAM.md
skills/bigscape/agents/openai.yaml
skills/bigscape/licenses/pku-metagenomics/LICENSE
skills/bigscape/references/upstream-docs/compute-setup.md
skills/bigscape/references/upstream-docs/getting-started.md
skills/bigscape/references/upstream-docs/multi-platform.md
skills/bigscape/references/upstream-docs/public-databases.md
skills/bigscape/references/upstream-docs/references.md
skills/bigscape/references/upstream-docs/skills.md
skills/bigscape/references/upstream-docs/standard-pipeline.md
skills/bigscape/references/upstream-docs/tool-selection.md
skills/bigscape/references/upstream-docs/troubleshooting.md
skills/binchicken/DNAKIT.md
skills/binchicken/SKILL.md
skills/binchicken/UPSTREAM.md
skills/binchicken/licenses/pku-metagenomics/LICENSE
skills/binchicken/references/upstream-docs/compute-setup.md
skills/binchicken/references/upstream-docs/getting-started.md
skills/binchicken/references/upstream-docs/multi-platform.md
skills/binchicken/references/upstream-docs/public-databases.md
skills/binchicken/references/upstream-docs/references.md
skills/binchicken/references/upstream-docs/skills.md
skills/binchicken/references/upstream-docs/standard-pipeline.md
skills/binchicken/references/upstream-docs/tool-selection.md
skills/binchicken/references/upstream-docs/troubleshooting.md
skills/binning-qc/DNAKIT.md
skills/binning-qc/SKILL.md
skills/binning-qc/UPSTREAM.md
skills/binning-qc/docs/README.md
skills/binning-qc/docs/checkm2.md
skills/binning-qc/docs/coverm.md
skills/binning-qc/docs/eukcc.md
skills/binning-qc/docs/gunc.md
skills/binning-qc/docs/metabat2.md
skills/binning-qc/docs/quickbin.md
skills/binning-qc/docs/semibin2.md
skills/binning-qc/fixtures/checkm2.tsv
skills/binning-qc/fixtures/domain_routing.tsv
skills/binning-qc/fixtures/eukcc.tsv
skills/binning-qc/fixtures/gtdbtk.tsv
skills/binning-qc/fixtures/gunc.tsv
skills/binning-qc/licenses/omics/LICENSE
skills/binning-qc/scripts/build_bin_qc_tables.py
skills/biobakery-databases/DNAKIT.md
skills/biobakery-databases/SKILL.md
skills/biobakery-databases/UPSTREAM.md
skills/biobakery-databases/agents/openai.yaml
skills/biobakery-databases/licenses/pku-metagenomics/LICENSE
skills/biobakery-databases/references/upstream-docs/compute-setup.md
skills/biobakery-databases/references/upstream-docs/getting-started.md
skills/biobakery-databases/references/upstream-docs/multi-platform.md
skills/biobakery-databases/references/upstream-docs/public-databases.md
skills/biobakery-databases/references/upstream-docs/references.md
skills/biobakery-databases/references/upstream-docs/skills.md
skills/biobakery-databases/references/upstream-docs/standard-pipeline.md
skills/biobakery-databases/references/upstream-docs/tool-selection.md
skills/biobakery-databases/references/upstream-docs/troubleshooting.md
skills/bioconductor-bridge/DNAKIT.md
skills/bioconductor-bridge/LICENSE
skills/bioconductor-bridge/SKILL.md
skills/bioconductor-bridge/UPSTREAM.md
skills/bioconductor-bridge/bioc_recommender.py
skills/bioconductor-bridge/bioconductor_bridge.py
skills/bioconductor-bridge/references/upstream-readme.md
skills/bioconductor-bridge/resources/clawbio/common/checksums.py
skills/bioconductor-bridge/tests/test_bioc_recommender.py
skills/bioconductor-bridge/tests/test_bioconductor_bridge.py
skills/bioinfo-pitfalls/DNAKIT.md
skills/bioinfo-pitfalls/SKILL.md
skills/bioinfo-pitfalls/UPSTREAM.md
skills/bioinfo-pitfalls/licenses/plant-skills/LICENSE
skills/bioinformatics-methods-results-writer/CHANGELOG.md
skills/bioinformatics-methods-results-writer/DNAKIT.md
skills/bioinformatics-methods-results-writer/SKILL.md
skills/bioinformatics-methods-results-writer/UPSTREAM.md
skills/bioinformatics-methods-results-writer/references.md
skills/bioinformatics-methods-results-writer/licenses/damlab/LICENSE
skills/bioinformatics-project/DNAKIT.md
skills/bioinformatics-project/SKILL.md
skills/bioinformatics-project/UPSTREAM.md
skills/bioinformatics-project/examples/environment.pixi.toml
skills/bioinformatics-project/examples/gitignore.example
skills/bioinformatics-project/examples/lab-notebook-entry.md
skills/bioinformatics-project/examples/project-tree.txt
skills/bioinformatics-project/examples/runall.sh
skills/bioinformatics-project/examples/samples.tsv
skills/bioinformatics-project/licenses/omics/LICENSE
skills/bioinformatics-project/references/environments.md
skills/bioinformatics-project/references/good-enough-practices.md
skills/bioinformatics-project/references/project-layout.md
skills/bioinformatics-project/references/reproducibility-checklist.md
skills/bioinformatics-project/scripts/scaffold_project.py
skills/biomart-queries/DNAKIT.md
skills/biomart-queries/SKILL.md
skills/biomart-queries/UPSTREAM.md
skills/biomart-queries/usage-guide.md
skills/biomart-queries/examples/bulk_id_mapping.py
skills/biomart-queries/examples/coordinate_table.sh
skills/biomart-queries/examples/ortholog_table.py
skills/biomart-queries/licenses/bioskills/LICENSE
skills/biomcp/AUTHORING.md
skills/biomcp/CITATION.cff
skills/biomcp/DNAKIT.md
skills/biomcp/LICENSE
skills/biomcp/SKILL.md
skills/biomcp/UPSTREAM.md
skills/biomcp/jq-examples.md
skills/biomcp/examples/get-gene-BRAF.json
skills/biomcp/examples/get-gene-BRAF.txt
skills/biomcp/examples/get-trial.json
skills/biomcp/examples/get-trial.txt
skills/biomcp/examples/get-variant-rs113488022-all.json
skills/biomcp/examples/get-variant-rs113488022-all.txt
skills/biomcp/examples/search-article.json
skills/biomcp/examples/search-article.txt
skills/biomcp/examples/search-drug.json
skills/biomcp/examples/search-drug.txt
skills/biomcp/references/upstream-readme.md
skills/biomcp/schemas/article.json
skills/biomcp/schemas/disease.json
skills/biomcp/schemas/drug.json
skills/biomcp/schemas/gene.json
skills/biomcp/schemas/pathway.json
skills/biomcp/schemas/trial.json
skills/biomcp/schemas/variant.json
skills/biomcp/schemas/workflow-ladder.schema.json
skills/biomcp/use-cases/01-treatment-lookup.md
skills/biomcp/use-cases/02-symptom-phenotype.md
skills/biomcp/use-cases/03-gene-disease-orientation.md
skills/biomcp/use-cases/04-article-follow-up.md
skills/biomcp/use-cases/05-variant-pathogenicity.md
skills/biomcp/use-cases/06-drug-regulatory.md
skills/biomcp/use-cases/07-gene-function-localization.md
skills/biomcp/use-cases/08-mechanism-pathway.md
skills/biomcp/use-cases/09-trial-recruitment.md
skills/biomcp/use-cases/10-pharmacogene-cumulative.md
skills/biomcp/use-cases/11-disease-locus-mapping.md
skills/biomcp/use-cases/12-cellular-process-regulation.md
skills/biomcp/use-cases/13-mutation-catalog.md
skills/biomcp/use-cases/14-syndrome-disambiguation.md
skills/biomcp/use-cases/15-negative-evidence.md
skills/biomcp/use-cases/16-normalize-to-codes.md
skills/biomcp/use-cases/17-exact-variant-literature.md
skills/biomcp/use-cases/_TEMPLATE.ladder.json
skills/biomcp/use-cases/_TEMPLATE.md
skills/biomcp/use-cases/article-follow-up.ladder.json
skills/biomcp/use-cases/mechanism-pathway.ladder.json
skills/biomcp/use-cases/mutation-catalog.ladder.json
skills/biomcp/use-cases/normalize-to-codes.ladder.json
skills/biomcp/use-cases/pharmacogene-cumulative.ladder.json
skills/biomcp/use-cases/treatment-lookup.ladder.json
skills/biomcp/use-cases/trial-recruitment.ladder.json
skills/biomcp/use-cases/variant-pathogenicity.ladder.json
skills/bioservices-multi-database/DNAKIT.md
skills/bioservices-multi-database/SKILL.md
skills/bioservices-multi-database/UPSTREAM.md
skills/bioservices-multi-database/licenses/kdense/CITATION.cff
skills/bioservices-multi-database/licenses/kdense/LICENSE.md
skills/bioservices-multi-database/licenses/sciagent/CC-BY-4.0.txt
skills/bioservices-multi-database/licenses/sciagent/LICENSE
skills/bioservices-multi-database/licenses/tooluniverse/LICENSE
skills/bioservices-multi-database/references/identifier_mapping_guide.md
skills/bioservices-multi-database/references/services_catalog.md
skills/biosurfdb/DNAKIT.md
skills/biosurfdb/SKILL.md
skills/biosurfdb/UPSTREAM.md
skills/biosurfdb/licenses/pku-metagenomics/LICENSE
skills/biosurfdb/references/upstream-docs/compute-setup.md
skills/biosurfdb/references/upstream-docs/getting-started.md
skills/biosurfdb/references/upstream-docs/multi-platform.md
skills/biosurfdb/references/upstream-docs/public-databases.md
skills/biosurfdb/references/upstream-docs/references.md
skills/biosurfdb/references/upstream-docs/skills.md
skills/biosurfdb/references/upstream-docs/standard-pipeline.md
skills/biosurfdb/references/upstream-docs/tool-selection.md
skills/biosurfdb/references/upstream-docs/troubleshooting.md
skills/blast-searches/DNAKIT.md
skills/blast-searches/SKILL.md
skills/blast-searches/UPSTREAM.md
skills/blast-searches/usage-guide.md
skills/blast-searches/examples/basic_blast.py
skills/blast-searches/examples/blastp_filtered.py
skills/blast-searches/examples/save_and_parse.py
skills/blast-searches/licenses/bioskills/LICENSE
skills/borzoi/DNAKIT.md
skills/borzoi/SKILL.md
skills/borzoi/UPSTREAM.md
skills/borzoi/licenses/feynman/LICENSE
skills/busco-assessor/DNAKIT.md
skills/busco-assessor/SKILL.md
skills/busco-assessor/UPSTREAM.md
skills/busco-assessor/busco_assessor.py
skills/busco-assessor/licenses/clawbio/CITATION.cff
skills/busco-assessor/licenses/clawbio/LICENSE
skills/busco-assessor/tests/__init__.py
skills/busco-assessor/tests/test_busco_assessor.py
skills/busco-status-interpretation/DNAKIT.md
skills/busco-status-interpretation/SKILL.md
skills/busco-status-interpretation/UPSTREAM.md
skills/busco-status-interpretation/licenses/kdense/CITATION.cff
skills/busco-status-interpretation/licenses/kdense/LICENSE.md
skills/busco-status-interpretation/licenses/sciagent/CC-BY-4.0.txt
skills/busco-status-interpretation/licenses/sciagent/LICENSE
skills/busco-status-interpretation/licenses/tooluniverse/LICENSE
skills/caduceus/DNAKIT.md
skills/caduceus/SKILL.md
skills/caduceus/UPSTREAM.md
skills/caduceus/licenses/pku-metagenomics/LICENSE
skills/caduceus/references/upstream-docs/compute-setup.md
skills/caduceus/references/upstream-docs/getting-started.md
skills/caduceus/references/upstream-docs/multi-platform.md
skills/caduceus/references/upstream-docs/public-databases.md
skills/caduceus/references/upstream-docs/references.md
skills/caduceus/references/upstream-docs/skills.md
skills/caduceus/references/upstream-docs/standard-pipeline.md
skills/caduceus/references/upstream-docs/tool-selection.md
skills/caduceus/references/upstream-docs/troubleshooting.md
skills/cami/DNAKIT.md
skills/cami/SKILL.md
skills/cami/UPSTREAM.md
skills/cami/licenses/pku-metagenomics/LICENSE
skills/cami/references/upstream-docs/compute-setup.md
skills/cami/references/upstream-docs/getting-started.md
skills/cami/references/upstream-docs/multi-platform.md
skills/cami/references/upstream-docs/public-databases.md
skills/cami/references/upstream-docs/references.md
skills/cami/references/upstream-docs/skills.md
skills/cami/references/upstream-docs/standard-pipeline.md
skills/cami/references/upstream-docs/tool-selection.md
skills/cami/references/upstream-docs/troubleshooting.md
skills/cancer-genomics-tcga/DNAKIT.md
skills/cancer-genomics-tcga/SKILL.md
skills/cancer-genomics-tcga/UPSTREAM.md
skills/cancer-genomics-tcga/licenses/tooluniverse/LICENSE
skills/cancer-variant-interpretation/ANALYSIS_DETAILS.md
skills/cancer-variant-interpretation/DNAKIT.md
skills/cancer-variant-interpretation/EXAMPLES.md
skills/cancer-variant-interpretation/INPUT_PARSING.md
skills/cancer-variant-interpretation/QUICK_START.md
skills/cancer-variant-interpretation/REPORT_TEMPLATE.md
skills/cancer-variant-interpretation/SCORING_TABLES.md
skills/cancer-variant-interpretation/SKILL.md
skills/cancer-variant-interpretation/TOOLS_REFERENCE.md
skills/cancer-variant-interpretation/UPSTREAM.md
skills/cancer-variant-interpretation/test_skill.py
skills/cancer-variant-interpretation/licenses/tooluniverse/LICENSE
skills/causal-genomics-colocalization-analysis/DNAKIT.md
skills/causal-genomics-colocalization-analysis/SKILL.md
skills/causal-genomics-colocalization-analysis/UPSTREAM.md
skills/causal-genomics-colocalization-analysis/usage-guide.md
skills/causal-genomics-colocalization-analysis/examples/coloc_abf_pipeline.R
skills/causal-genomics-colocalization-analysis/examples/coloc_analysis.R
skills/causal-genomics-colocalization-analysis/examples/coloc_susie.R
skills/causal-genomics-colocalization-analysis/examples/coloc_susie_multicausal.R
skills/causal-genomics-colocalization-analysis/examples/regional_plots.R
skills/causal-genomics-colocalization-analysis/licenses/bioskills/LICENSE
skills/causal-genomics-effector-gene-prioritization/DNAKIT.md
skills/causal-genomics-effector-gene-prioritization/SKILL.md
skills/causal-genomics-effector-gene-prioritization/UPSTREAM.md
skills/causal-genomics-effector-gene-prioritization/usage-guide.md
skills/causal-genomics-effector-gene-prioritization/examples/magma_genebased.sh
skills/causal-genomics-effector-gene-prioritization/examples/multi_evidence_integration.R
skills/causal-genomics-effector-gene-prioritization/licenses/bioskills/LICENSE
skills/causal-genomics-fine-mapping/DNAKIT.md
skills/causal-genomics-fine-mapping/SKILL.md
skills/causal-genomics-fine-mapping/UPSTREAM.md
skills/causal-genomics-fine-mapping/usage-guide.md
skills/causal-genomics-fine-mapping/examples/finemap_pipeline.sh
skills/causal-genomics-fine-mapping/examples/pip_visualization.R
skills/causal-genomics-fine-mapping/examples/susie_finemapping.R
skills/causal-genomics-fine-mapping/examples/susie_rss_finemap.R
skills/causal-genomics-fine-mapping/examples/susiex_multiancestry.sh
skills/causal-genomics-fine-mapping/licenses/bioskills/LICENSE
skills/causal-genomics-genetic-correlation/DNAKIT.md
skills/causal-genomics-genetic-correlation/SKILL.md
skills/causal-genomics-genetic-correlation/UPSTREAM.md
skills/causal-genomics-genetic-correlation/usage-guide.md
skills/causal-genomics-genetic-correlation/examples/lava_local_rg.R
skills/causal-genomics-genetic-correlation/examples/ldsc_crosstrait_rg.sh
skills/causal-genomics-genetic-correlation/licenses/bioskills/LICENSE
skills/causal-genomics-genomic-sem/DNAKIT.md
skills/causal-genomics-genomic-sem/SKILL.md
skills/causal-genomics-genomic-sem/UPSTREAM.md
skills/causal-genomics-genomic-sem/usage-guide.md
skills/causal-genomics-genomic-sem/examples/genomic_sem_commonfactor.R
skills/causal-genomics-genomic-sem/examples/mtag_pipeline.sh
skills/causal-genomics-genomic-sem/licenses/bioskills/LICENSE
skills/causal-genomics-heritability-partitioning/DNAKIT.md
skills/causal-genomics-heritability-partitioning/SKILL.md
skills/causal-genomics-heritability-partitioning/UPSTREAM.md
skills/causal-genomics-heritability-partitioning/usage-guide.md
skills/causal-genomics-heritability-partitioning/examples/ldak_sumher.sh
skills/causal-genomics-heritability-partitioning/examples/ldsc_partitioned_h2.sh
skills/causal-genomics-heritability-partitioning/licenses/bioskills/LICENSE
skills/causal-genomics-mediation-analysis/DNAKIT.md
skills/causal-genomics-mediation-analysis/SKILL.md
skills/causal-genomics-mediation-analysis/UPSTREAM.md
skills/causal-genomics-mediation-analysis/usage-guide.md
skills/causal-genomics-mediation-analysis/examples/cmaverse_4way.R
skills/causal-genomics-mediation-analysis/examples/eqtl_mediation.R
skills/causal-genomics-mediation-analysis/examples/mvmr_mediation.R
skills/causal-genomics-mediation-analysis/examples/sensitivity_analysis.R
skills/causal-genomics-mediation-analysis/licenses/bioskills/LICENSE
skills/causal-genomics-mendelian-randomization/DNAKIT.md
skills/causal-genomics-mendelian-randomization/SKILL.md
skills/causal-genomics-mendelian-randomization/UPSTREAM.md
skills/causal-genomics-mendelian-randomization/usage-guide.md
skills/causal-genomics-mendelian-randomization/examples/cis_mr_drug_target.R
skills/causal-genomics-mendelian-randomization/examples/mr_visualization.R
skills/causal-genomics-mendelian-randomization/examples/two_sample_mr.R
skills/causal-genomics-mendelian-randomization/examples/twosamplemr_analysis.R
skills/causal-genomics-mendelian-randomization/licenses/bioskills/LICENSE
skills/causal-genomics-pleiotropy-detection/DNAKIT.md
skills/causal-genomics-pleiotropy-detection/SKILL.md
skills/causal-genomics-pleiotropy-detection/UPSTREAM.md
skills/causal-genomics-pleiotropy-detection/usage-guide.md
skills/causal-genomics-pleiotropy-detection/examples/bidirectional_mr.R
skills/causal-genomics-pleiotropy-detection/examples/cause_analysis.R
skills/causal-genomics-pleiotropy-detection/examples/mr_presso_analysis.R
skills/causal-genomics-pleiotropy-detection/examples/sensitivity_battery.R
skills/causal-genomics-pleiotropy-detection/examples/simex_egger_correction.R
skills/causal-genomics-pleiotropy-detection/licenses/bioskills/LICENSE
skills/causal-genomics-proteome-mr-drug-target/DNAKIT.md
skills/causal-genomics-proteome-mr-drug-target/SKILL.md
skills/causal-genomics-proteome-mr-drug-target/UPSTREAM.md
skills/causal-genomics-proteome-mr-drug-target/usage-guide.md
skills/causal-genomics-proteome-mr-drug-target/examples/cis_pqtl_mr.R
skills/causal-genomics-proteome-mr-drug-target/examples/phewas_drug_target_mr.R
skills/causal-genomics-proteome-mr-drug-target/licenses/bioskills/LICENSE
skills/causal-genomics-transcriptome-wide-association/DNAKIT.md
skills/causal-genomics-transcriptome-wide-association/SKILL.md
skills/causal-genomics-transcriptome-wide-association/UPSTREAM.md
skills/causal-genomics-transcriptome-wide-association/usage-guide.md
skills/causal-genomics-transcriptome-wide-association/examples/focus_finemap.sh
skills/causal-genomics-transcriptome-wide-association/examples/s_predixcan_pipeline.sh
skills/causal-genomics-transcriptome-wide-association/licenses/bioskills/LICENSE
skills/cbioportal-database/DNAKIT.md
skills/cbioportal-database/SKILL.md
skills/cbioportal-database/UPSTREAM.md
skills/cbioportal-database/licenses/kdense/CITATION.cff
skills/cbioportal-database/licenses/kdense/LICENSE.md
skills/cbioportal-database/licenses/sciagent/CC-BY-4.0.txt
skills/cbioportal-database/licenses/sciagent/LICENSE
skills/cbioportal-database/licenses/tooluniverse/LICENSE
skills/cfdna-preprocessing/DNAKIT.md
skills/cfdna-preprocessing/SKILL.md
skills/cfdna-preprocessing/UPSTREAM.md
skills/cfdna-preprocessing/usage-guide.md
skills/cfdna-preprocessing/examples/preprocess_cfdna.py
skills/cfdna-preprocessing/licenses/bioskills/LICENSE
skills/checkm2/DNAKIT.md
skills/checkm2/SKILL.md
skills/checkm2/UPSTREAM.md
skills/checkm2/agents/openai.yaml
skills/checkm2/licenses/pku-metagenomics/LICENSE
skills/checkm2/references/upstream-docs/compute-setup.md
skills/checkm2/references/upstream-docs/getting-started.md
skills/checkm2/references/upstream-docs/multi-platform.md
skills/checkm2/references/upstream-docs/public-databases.md
skills/checkm2/references/upstream-docs/references.md
skills/checkm2/references/upstream-docs/skills.md
skills/checkm2/references/upstream-docs/standard-pipeline.md
skills/checkm2/references/upstream-docs/tool-selection.md
skills/checkm2/references/upstream-docs/troubleshooting.md
skills/checkv/DNAKIT.md
skills/checkv/SKILL.md
skills/checkv/UPSTREAM.md
skills/checkv/agents/openai.yaml
skills/checkv/licenses/pku-metagenomics/LICENSE
skills/checkv/references/upstream-docs/compute-setup.md
skills/checkv/references/upstream-docs/getting-started.md
skills/checkv/references/upstream-docs/multi-platform.md
skills/checkv/references/upstream-docs/public-databases.md
skills/checkv/references/upstream-docs/references.md
skills/checkv/references/upstream-docs/skills.md
skills/checkv/references/upstream-docs/standard-pipeline.md
skills/checkv/references/upstream-docs/tool-selection.md
skills/checkv/references/upstream-docs/troubleshooting.md
skills/chip-atlas-diff-analysis/DNAKIT.md
skills/chip-atlas-diff-analysis/SKILL.md
skills/chip-atlas-diff-analysis/UPSTREAM.md
skills/chip-atlas-diff-analysis/licenses/agentic-science/LICENSE
skills/chip-atlas-diff-analysis/references/diff_api_format.md
skills/chip-atlas-diff-analysis/references/output_format.md
skills/chip-atlas-diff-analysis/references/statistical_methods.md
skills/chip-atlas-diff-analysis/scripts/__init__.py
skills/chip-atlas-diff-analysis/scripts/annotate_genes.py
skills/chip-atlas-diff-analysis/scripts/export_all.py
skills/chip-atlas-diff-analysis/scripts/filter_regions.py
skills/chip-atlas-diff-analysis/scripts/generate_all_plots.py
skills/chip-atlas-diff-analysis/scripts/load_example_data.py
skills/chip-atlas-diff-analysis/scripts/load_user_data.py
skills/chip-atlas-diff-analysis/scripts/parse_diff_bed.py
skills/chip-atlas-diff-analysis/scripts/qc_checks.py
skills/chip-atlas-diff-analysis/scripts/query_chip_atlas_diff.py
skills/chip-atlas-diff-analysis/scripts/run_diff_workflow.py
skills/chip-atlas-peak-enrichment/DNAKIT.md
skills/chip-atlas-peak-enrichment/SKILL.md
skills/chip-atlas-peak-enrichment/UPSTREAM.md
skills/chip-atlas-peak-enrichment/licenses/agentic-science/LICENSE
skills/chip-atlas-peak-enrichment/references/api_format.md
skills/chip-atlas-peak-enrichment/references/enrichment_statistics.md
skills/chip-atlas-peak-enrichment/references/peak_thresholds.md
skills/chip-atlas-peak-enrichment/references/promoter_definitions.md
skills/chip-atlas-peak-enrichment/scripts/__init__.py
skills/chip-atlas-peak-enrichment/scripts/convert_genes_to_regions.py
skills/chip-atlas-peak-enrichment/scripts/export_all.py
skills/chip-atlas-peak-enrichment/scripts/filter_experiments.py
skills/chip-atlas-peak-enrichment/scripts/generate_all_plots.py
skills/chip-atlas-peak-enrichment/scripts/load_example_data.py
skills/chip-atlas-peak-enrichment/scripts/load_user_data.py
skills/chip-atlas-peak-enrichment/scripts/query_chip_atlas_enrichment.py
skills/chip-atlas-peak-enrichment/scripts/run_enrichment_workflow.py
skills/chip-atlas-target-genes/DNAKIT.md
skills/chip-atlas-target-genes/SKILL.md
skills/chip-atlas-target-genes/UPSTREAM.md
skills/chip-atlas-target-genes/licenses/agentic-science/LICENSE
skills/chip-atlas-target-genes/references/macs2_binding_scores.md
skills/chip-atlas-target-genes/references/string_scores.md
skills/chip-atlas-target-genes/references/target_genes_data_format.md
skills/chip-atlas-target-genes/scripts/__init__.py
skills/chip-atlas-target-genes/scripts/download_target_genes.py
skills/chip-atlas-target-genes/scripts/export_all.py
skills/chip-atlas-target-genes/scripts/filter_targets.py
skills/chip-atlas-target-genes/scripts/generate_all_plots.py
skills/chip-atlas-target-genes/scripts/load_example_query.py
skills/chip-atlas-target-genes/scripts/load_user_query.py
skills/chip-atlas-target-genes/scripts/run_target_genes_workflow.py
skills/chipseq-allele-specific-binding/DNAKIT.md
skills/chipseq-allele-specific-binding/SKILL.md
skills/chipseq-allele-specific-binding/UPSTREAM.md
skills/chipseq-allele-specific-binding/usage-guide.md
skills/chipseq-allele-specific-binding/examples/baalchip_workflow.R
skills/chipseq-allele-specific-binding/licenses/bioskills/LICENSE
skills/chipseq-chip-deep-learning/DNAKIT.md
skills/chipseq-chip-deep-learning/SKILL.md
skills/chipseq-chip-deep-learning/UPSTREAM.md
skills/chipseq-chip-deep-learning/usage-guide.md
skills/chipseq-chip-deep-learning/examples/chrombpnet_variant_effect.py
skills/chipseq-chip-deep-learning/licenses/bioskills/LICENSE
skills/chipseq-chromatin-state-segmentation/DNAKIT.md
skills/chipseq-chromatin-state-segmentation/SKILL.md
skills/chipseq-chromatin-state-segmentation/UPSTREAM.md
skills/chipseq-chromatin-state-segmentation/usage-guide.md
skills/chipseq-chromatin-state-segmentation/examples/chromhmm_pipeline.sh
skills/chipseq-chromatin-state-segmentation/licenses/bioskills/LICENSE
skills/chipseq-cut-and-run-tag/DNAKIT.md
skills/chipseq-cut-and-run-tag/SKILL.md
skills/chipseq-cut-and-run-tag/UPSTREAM.md
skills/chipseq-cut-and-run-tag/usage-guide.md
skills/chipseq-cut-and-run-tag/examples/cutandrun_pipeline.sh
skills/chipseq-cut-and-run-tag/licenses/bioskills/LICENSE
skills/chipseq-differential-binding/DNAKIT.md
skills/chipseq-differential-binding/SKILL.md
skills/chipseq-differential-binding/UPSTREAM.md
skills/chipseq-differential-binding/usage-guide.md
skills/chipseq-differential-binding/examples/csaw_windows_diff.R
skills/chipseq-differential-binding/examples/deseq2_from_counts.R
skills/chipseq-differential-binding/examples/diffbind_analysis.R
skills/chipseq-differential-binding/examples/pydeseq2_from_counts.py
skills/chipseq-differential-binding/licenses/bioskills/LICENSE
skills/chipseq-motif-analysis/DNAKIT.md
skills/chipseq-motif-analysis/SKILL.md
skills/chipseq-motif-analysis/UPSTREAM.md
skills/chipseq-motif-analysis/usage-guide.md
skills/chipseq-motif-analysis/examples/motif_analysis.sh
skills/chipseq-motif-analysis/licenses/bioskills/LICENSE
skills/chipseq-peak-annotation/DNAKIT.md
skills/chipseq-peak-annotation/SKILL.md
skills/chipseq-peak-annotation/UPSTREAM.md
skills/chipseq-peak-annotation/usage-guide.md
skills/chipseq-peak-annotation/examples/annotate_peaks.R
skills/chipseq-peak-annotation/examples/annotate_peaks.py
skills/chipseq-peak-annotation/licenses/bioskills/LICENSE
skills/chipseq-peak-calling/DNAKIT.md
skills/chipseq-peak-calling/SKILL.md
skills/chipseq-peak-calling/UPSTREAM.md
skills/chipseq-peak-calling/usage-guide.md
skills/chipseq-peak-calling/examples/macs3_peak_calling.sh
skills/chipseq-peak-calling/licenses/bioskills/LICENSE
skills/chipseq-qc/DNAKIT.md
skills/chipseq-qc/SKILL.md
skills/chipseq-qc/UPSTREAM.md
skills/chipseq-qc/usage-guide.md
skills/chipseq-qc/examples/calculate_frip.sh
skills/chipseq-qc/examples/chipseq_qc.py
skills/chipseq-qc/examples/run_idr.sh
skills/chipseq-qc/licenses/bioskills/LICENSE
skills/chipseq-spike-in-normalization/DNAKIT.md
skills/chipseq-spike-in-normalization/SKILL.md
skills/chipseq-spike-in-normalization/UPSTREAM.md
skills/chipseq-spike-in-normalization/usage-guide.md
skills/chipseq-spike-in-normalization/examples/spikein_chiprx_diffbind.R
skills/chipseq-spike-in-normalization/licenses/bioskills/LICENSE
skills/chipseq-super-enhancers/DNAKIT.md
skills/chipseq-super-enhancers/SKILL.md
skills/chipseq-super-enhancers/UPSTREAM.md
skills/chipseq-super-enhancers/usage-guide.md
skills/chipseq-super-enhancers/examples/analyze_super_enhancers.py
skills/chipseq-super-enhancers/examples/run_rose.sh
skills/chipseq-super-enhancers/licenses/bioskills/LICENSE
skills/chipseq-visualization/DNAKIT.md
skills/chipseq-visualization/SKILL.md
skills/chipseq-visualization/UPSTREAM.md
skills/chipseq-visualization/usage-guide.md
skills/chipseq-visualization/examples/chipseeker_profile.R
skills/chipseq-visualization/examples/deeptools_heatmap.sh
skills/chipseq-visualization/licenses/bioskills/LICENSE
skills/cite-encode/DNAKIT.md
skills/cite-encode/SKILL.md
skills/cite-encode/UPSTREAM.md
skills/cite-encode/licenses/encode-toolkit/CITATION.cff
skills/cite-encode/licenses/encode-toolkit/LICENSE
skills/cite-encode/references/literature.md
skills/clinical-databases-acmg-classification/DNAKIT.md
skills/clinical-databases-acmg-classification/SKILL.md
skills/clinical-databases-acmg-classification/UPSTREAM.md
skills/clinical-databases-acmg-classification/usage-guide.md
skills/clinical-databases-acmg-classification/examples/acmg_classify.py
skills/clinical-databases-acmg-classification/licenses/bioskills/LICENSE
skills/clinical-databases-clinvar-lookup/DNAKIT.md
skills/clinical-databases-clinvar-lookup/SKILL.md
skills/clinical-databases-clinvar-lookup/UPSTREAM.md
skills/clinical-databases-clinvar-lookup/usage-guide.md
skills/clinical-databases-clinvar-lookup/examples/clinvar_query.py
skills/clinical-databases-clinvar-lookup/licenses/bioskills/LICENSE
skills/clinical-databases-dbsnp-queries/DNAKIT.md
skills/clinical-databases-dbsnp-queries/SKILL.md
skills/clinical-databases-dbsnp-queries/UPSTREAM.md
skills/clinical-databases-dbsnp-queries/usage-guide.md
skills/clinical-databases-dbsnp-queries/examples/dbsnp_lookup.py
skills/clinical-databases-dbsnp-queries/licenses/bioskills/LICENSE
skills/clinical-databases-gnomad-frequencies/DNAKIT.md
skills/clinical-databases-gnomad-frequencies/SKILL.md
skills/clinical-databases-gnomad-frequencies/UPSTREAM.md
skills/clinical-databases-gnomad-frequencies/usage-guide.md
skills/clinical-databases-gnomad-frequencies/examples/gnomad_query.py
skills/clinical-databases-gnomad-frequencies/licenses/bioskills/LICENSE
skills/clinical-databases-hla-typing/DNAKIT.md
skills/clinical-databases-hla-typing/SKILL.md
skills/clinical-databases-hla-typing/UPSTREAM.md
skills/clinical-databases-hla-typing/usage-guide.md
skills/clinical-databases-hla-typing/examples/optitype_workflow.sh
skills/clinical-databases-hla-typing/examples/t1k_workflow.sh
skills/clinical-databases-hla-typing/licenses/bioskills/LICENSE
skills/clinical-databases-msi-detection/DNAKIT.md
skills/clinical-databases-msi-detection/SKILL.md
skills/clinical-databases-msi-detection/UPSTREAM.md
skills/clinical-databases-msi-detection/usage-guide.md
skills/clinical-databases-msi-detection/examples/msi_detection.sh
skills/clinical-databases-msi-detection/licenses/bioskills/LICENSE
skills/clinical-databases-myvariant-queries/DNAKIT.md
skills/clinical-databases-myvariant-queries/SKILL.md
skills/clinical-databases-myvariant-queries/UPSTREAM.md
skills/clinical-databases-myvariant-queries/usage-guide.md
skills/clinical-databases-myvariant-queries/examples/query_myvariant.py
skills/clinical-databases-myvariant-queries/licenses/bioskills/LICENSE
skills/clinical-databases-pharmacogenomics/DNAKIT.md
skills/clinical-databases-pharmacogenomics/SKILL.md
skills/clinical-databases-pharmacogenomics/UPSTREAM.md
skills/clinical-databases-pharmacogenomics/usage-guide.md
skills/clinical-databases-pharmacogenomics/examples/pharmgkb_query.py
skills/clinical-databases-pharmacogenomics/licenses/bioskills/LICENSE
skills/clinical-databases-polygenic-risk/DNAKIT.md
skills/clinical-databases-polygenic-risk/SKILL.md
skills/clinical-databases-polygenic-risk/UPSTREAM.md
skills/clinical-databases-polygenic-risk/usage-guide.md
skills/clinical-databases-polygenic-risk/examples/ldpred2_analysis.R
skills/clinical-databases-polygenic-risk/examples/prsice2_workflow.sh
skills/clinical-databases-polygenic-risk/licenses/bioskills/LICENSE
skills/clinical-databases-somatic-signatures/DNAKIT.md
skills/clinical-databases-somatic-signatures/SKILL.md
skills/clinical-databases-somatic-signatures/UPSTREAM.md
skills/clinical-databases-somatic-signatures/usage-guide.md
skills/clinical-databases-somatic-signatures/examples/mutsig_fitting.R
skills/clinical-databases-somatic-signatures/examples/sigprofiler_analysis.py
skills/clinical-databases-somatic-signatures/licenses/bioskills/LICENSE
skills/clinical-databases-tumor-mutational-burden/DNAKIT.md
skills/clinical-databases-tumor-mutational-burden/SKILL.md
skills/clinical-databases-tumor-mutational-burden/UPSTREAM.md
skills/clinical-databases-tumor-mutational-burden/usage-guide.md
skills/clinical-databases-tumor-mutational-burden/examples/tmb_calculation.py
skills/clinical-databases-tumor-mutational-burden/licenses/bioskills/LICENSE
skills/clinical-databases-variant-prioritization/DNAKIT.md
skills/clinical-databases-variant-prioritization/SKILL.md
skills/clinical-databases-variant-prioritization/UPSTREAM.md
skills/clinical-databases-variant-prioritization/usage-guide.md
skills/clinical-databases-variant-prioritization/examples/prioritize_variants.py
skills/clinical-databases-variant-prioritization/licenses/bioskills/LICENSE
skills/clinpgx/DNAKIT.md
skills/clinpgx/INTENTS.json
skills/clinpgx/SKILL.md
skills/clinpgx/UPSTREAM.md
skills/clinpgx/api.py
skills/clinpgx/clinpgx.py
skills/clinpgx/licenses/clawbio/CITATION.cff
skills/clinpgx/licenses/clawbio/LICENSE
skills/clinpgx/tests/__init__.py
skills/clinpgx/tests/test_clinpgx.py
skills/codon-usage/DNAKIT.md
skills/codon-usage/SKILL.md
skills/codon-usage/UPSTREAM.md
skills/codon-usage/usage-guide.md
skills/codon-usage/examples/basic_analysis.py
skills/codon-usage/examples/cai_optimization.py
skills/codon-usage/examples/rscu_analysis.py
skills/codon-usage/licenses/bioskills/LICENSE
skills/comparative-genomics/DNAKIT.md
skills/comparative-genomics/SKILL.md
skills/comparative-genomics/UPSTREAM.md
skills/comparative-genomics-ancestral-reconstruction/DNAKIT.md
skills/comparative-genomics-ancestral-reconstruction/SKILL.md
skills/comparative-genomics-ancestral-reconstruction/UPSTREAM.md
skills/comparative-genomics-ancestral-reconstruction/usage-guide.md
skills/comparative-genomics-ancestral-reconstruction/examples/ancestral_reconstruction.py
skills/comparative-genomics-ancestral-reconstruction/licenses/bioskills/LICENSE
skills/comparative-genomics-comparative-annotation-projection/DNAKIT.md
skills/comparative-genomics-comparative-annotation-projection/SKILL.md
skills/comparative-genomics-comparative-annotation-projection/UPSTREAM.md
skills/comparative-genomics-comparative-annotation-projection/usage-guide.md
skills/comparative-genomics-comparative-annotation-projection/examples/toga_annotation_projection.sh
skills/comparative-genomics-comparative-annotation-projection/licenses/bioskills/LICENSE
skills/comparative-genomics-gene-family-evolution/DNAKIT.md
skills/comparative-genomics-gene-family-evolution/SKILL.md
skills/comparative-genomics-gene-family-evolution/UPSTREAM.md
skills/comparative-genomics-gene-family-evolution/usage-guide.md
skills/comparative-genomics-gene-family-evolution/examples/cafe5_birth_death_analysis.sh
skills/comparative-genomics-gene-family-evolution/licenses/bioskills/LICENSE
skills/comparative-genomics-gene-tree-species-tree-reconciliation/DNAKIT.md
skills/comparative-genomics-gene-tree-species-tree-reconciliation/SKILL.md
skills/comparative-genomics-gene-tree-species-tree-reconciliation/UPSTREAM.md
skills/comparative-genomics-gene-tree-species-tree-reconciliation/usage-guide.md
skills/comparative-genomics-gene-tree-species-tree-reconciliation/examples/ale_dtl_reconciliation.sh
skills/comparative-genomics-gene-tree-species-tree-reconciliation/licenses/bioskills/LICENSE
skills/comparative-genomics-genome-distance-and-species-delineation/DNAKIT.md
skills/comparative-genomics-genome-distance-and-species-delineation/SKILL.md
skills/comparative-genomics-genome-distance-and-species-delineation/UPSTREAM.md
skills/comparative-genomics-genome-distance-and-species-delineation/usage-guide.md
skills/comparative-genomics-genome-distance-and-species-delineation/examples/skani_ani_species_delineation.sh
skills/comparative-genomics-genome-distance-and-species-delineation/licenses/bioskills/LICENSE
skills/comparative-genomics-hgt-detection/DNAKIT.md
skills/comparative-genomics-hgt-detection/SKILL.md
skills/comparative-genomics-hgt-detection/UPSTREAM.md
skills/comparative-genomics-hgt-detection/usage-guide.md
skills/comparative-genomics-hgt-detection/examples/hgt_detection.py
skills/comparative-genomics-hgt-detection/licenses/bioskills/LICENSE
skills/comparative-genomics-introgression-detection/DNAKIT.md
skills/comparative-genomics-introgression-detection/SKILL.md
skills/comparative-genomics-introgression-detection/UPSTREAM.md
skills/comparative-genomics-introgression-detection/usage-guide.md
skills/comparative-genomics-introgression-detection/examples/dsuite_abba_baba_workflow.sh
skills/comparative-genomics-introgression-detection/licenses/bioskills/LICENSE
skills/comparative-genomics-ortholog-inference/DNAKIT.md
skills/comparative-genomics-ortholog-inference/SKILL.md
skills/comparative-genomics-ortholog-inference/UPSTREAM.md
skills/comparative-genomics-ortholog-inference/usage-guide.md
skills/comparative-genomics-ortholog-inference/examples/ortholog_analysis.py
skills/comparative-genomics-ortholog-inference/licenses/bioskills/LICENSE
skills/comparative-genomics-pangenome-analysis/DNAKIT.md
skills/comparative-genomics-pangenome-analysis/SKILL.md
skills/comparative-genomics-pangenome-analysis/UPSTREAM.md
skills/comparative-genomics-pangenome-analysis/usage-guide.md
skills/comparative-genomics-pangenome-analysis/examples/panaroo_bacterial_pangenome.sh
skills/comparative-genomics-pangenome-analysis/licenses/bioskills/LICENSE
skills/comparative-genomics-positive-selection/DNAKIT.md
skills/comparative-genomics-positive-selection/SKILL.md
skills/comparative-genomics-positive-selection/UPSTREAM.md
skills/comparative-genomics-positive-selection/usage-guide.md
skills/comparative-genomics-positive-selection/examples/selection_analysis.py
skills/comparative-genomics-positive-selection/licenses/bioskills/LICENSE
skills/comparative-genomics-synteny-analysis/DNAKIT.md
skills/comparative-genomics-synteny-analysis/SKILL.md
skills/comparative-genomics-synteny-analysis/UPSTREAM.md
skills/comparative-genomics-synteny-analysis/usage-guide.md
skills/comparative-genomics-synteny-analysis/examples/synteny_analysis.py
skills/comparative-genomics-synteny-analysis/licenses/bioskills/LICENSE
skills/comparative-genomics-whole-genome-alignment/DNAKIT.md
skills/comparative-genomics-whole-genome-alignment/SKILL.md
skills/comparative-genomics-whole-genome-alignment/UPSTREAM.md
skills/comparative-genomics-whole-genome-alignment/usage-guide.md
skills/comparative-genomics-whole-genome-alignment/examples/progressive_cactus_wga.sh
skills/comparative-genomics-whole-genome-alignment/licenses/bioskills/LICENSE
skills/comparative-genomics-whole-genome-duplication/DNAKIT.md
skills/comparative-genomics-whole-genome-duplication/SKILL.md
skills/comparative-genomics-whole-genome-duplication/UPSTREAM.md
skills/comparative-genomics-whole-genome-duplication/usage-guide.md
skills/comparative-genomics-whole-genome-duplication/examples/wgd_v2_ks_pipeline.sh
skills/comparative-genomics-whole-genome-duplication/licenses/bioskills/LICENSE
skills/comparative-genomics/licenses/tooluniverse/LICENSE
skills/comparative-genomics/scripts/dnds.py
skills/compare-biosamples/DNAKIT.md
skills/compare-biosamples/SKILL.md
skills/compare-biosamples/UPSTREAM.md
skills/compare-biosamples/licenses/encode-toolkit/CITATION.cff
skills/compare-biosamples/licenses/encode-toolkit/LICENSE
skills/compare-biosamples/references/literature.md
skills/compressed-files/DNAKIT.md
skills/compressed-files/SKILL.md
skills/compressed-files/UPSTREAM.md
skills/compressed-files/usage-guide.md
skills/compressed-files/examples/compressed_io.py
skills/compressed-files/licenses/bioskills/LICENSE
skills/consensus-sequences/DNAKIT.md
skills/consensus-sequences/SKILL.md
skills/consensus-sequences/UPSTREAM.md
skills/consensus-sequences/usage-guide.md
skills/consensus-sequences/examples/generate_consensus.sh
skills/consensus-sequences/licenses/bioskills/LICENSE
skills/copy-number-allele-specific-copy-number/DNAKIT.md
skills/copy-number-allele-specific-copy-number/SKILL.md
skills/copy-number-allele-specific-copy-number/UPSTREAM.md
skills/copy-number-allele-specific-copy-number/usage-guide.md
skills/copy-number-allele-specific-copy-number/examples/run_facets.R
skills/copy-number-allele-specific-copy-number/licenses/bioskills/LICENSE
skills/copy-number-cnv-annotation/DNAKIT.md
skills/copy-number-cnv-annotation/SKILL.md
skills/copy-number-cnv-annotation/UPSTREAM.md
skills/copy-number-cnv-annotation/usage-guide.md
skills/copy-number-cnv-annotation/examples/annotate_cnvs.py
skills/copy-number-cnv-annotation/licenses/bioskills/LICENSE
skills/copy-number-cnv-visualization/DNAKIT.md
skills/copy-number-cnv-visualization/SKILL.md
skills/copy-number-cnv-visualization/UPSTREAM.md
skills/copy-number-cnv-visualization/usage-guide.md
skills/copy-number-cnv-visualization/examples/plot_cnv.py
skills/copy-number-cnv-visualization/licenses/bioskills/LICENSE
skills/copy-number-cnvkit-analysis/DNAKIT.md
skills/copy-number-cnvkit-analysis/SKILL.md
skills/copy-number-cnvkit-analysis/UPSTREAM.md
skills/copy-number-cnvkit-analysis/usage-guide.md
skills/copy-number-cnvkit-analysis/examples/run_cnvkit.sh
skills/copy-number-cnvkit-analysis/licenses/bioskills/LICENSE
skills/copy-number-copy-ratio-segmentation/DNAKIT.md
skills/copy-number-copy-ratio-segmentation/SKILL.md
skills/copy-number-copy-ratio-segmentation/UPSTREAM.md
skills/copy-number-copy-ratio-segmentation/usage-guide.md
skills/copy-number-copy-ratio-segmentation/examples/segment_cbs.R
skills/copy-number-copy-ratio-segmentation/licenses/bioskills/LICENSE
skills/copy-number-focal-amplification-ecdna/DNAKIT.md
skills/copy-number-focal-amplification-ecdna/SKILL.md
skills/copy-number-focal-amplification-ecdna/UPSTREAM.md
skills/copy-number-focal-amplification-ecdna/usage-guide.md
skills/copy-number-focal-amplification-ecdna/examples/run_ampliconsuite.sh
skills/copy-number-focal-amplification-ecdna/licenses/bioskills/LICENSE
skills/copy-number-gatk-cnv/DNAKIT.md
skills/copy-number-gatk-cnv/SKILL.md
skills/copy-number-gatk-cnv/UPSTREAM.md
skills/copy-number-gatk-cnv/usage-guide.md
skills/copy-number-gatk-cnv/examples/run_gatk_cnv.sh
skills/copy-number-gatk-cnv/licenses/bioskills/LICENSE
skills/copy-number-germline-cnv-interpretation/DNAKIT.md
skills/copy-number-germline-cnv-interpretation/SKILL.md
skills/copy-number-germline-cnv-interpretation/UPSTREAM.md
skills/copy-number-germline-cnv-interpretation/usage-guide.md
skills/copy-number-germline-cnv-interpretation/examples/classify_germline_cnv.py
skills/copy-number-germline-cnv-interpretation/licenses/bioskills/LICENSE
skills/copy-number-hrd-scoring/DNAKIT.md
skills/copy-number-hrd-scoring/SKILL.md
skills/copy-number-hrd-scoring/UPSTREAM.md
skills/copy-number-hrd-scoring/usage-guide.md
skills/copy-number-hrd-scoring/examples/compute_hrd.R
skills/copy-number-hrd-scoring/licenses/bioskills/LICENSE
skills/copy-number-recurrent-cnv/DNAKIT.md
skills/copy-number-recurrent-cnv/SKILL.md
skills/copy-number-recurrent-cnv/UPSTREAM.md
skills/copy-number-recurrent-cnv/usage-guide.md
skills/copy-number-recurrent-cnv/examples/run_gistic2.sh
skills/copy-number-recurrent-cnv/licenses/bioskills/LICENSE
skills/copy-number-subclonal-copy-number/DNAKIT.md
skills/copy-number-subclonal-copy-number/SKILL.md
skills/copy-number-subclonal-copy-number/UPSTREAM.md
skills/copy-number-subclonal-copy-number/usage-guide.md
skills/copy-number-subclonal-copy-number/examples/run_titan.R
skills/copy-number-subclonal-copy-number/licenses/bioskills/LICENSE
skills/cosmic-database/DNAKIT.md
skills/cosmic-database/SKILL.md
skills/cosmic-database/UPSTREAM.md
skills/cosmic-database/licenses/kdense/CITATION.cff
skills/cosmic-database/licenses/kdense/LICENSE.md
skills/cosmic-database/licenses/sciagent/CC-BY-4.0.txt
skills/cosmic-database/licenses/sciagent/LICENSE
skills/cosmic-database/licenses/tooluniverse/LICENSE
skills/crispr-screen-triage/DNAKIT.md
skills/crispr-screen-triage/SKILL.md
skills/crispr-screen-triage/UPSTREAM.md
skills/crispr-screen-triage/crispr_screen_triage.py
skills/crispr-screen-triage/demo_screen_counts.csv
skills/crispr-screen-triage/licenses/clawbio/CITATION.cff
skills/crispr-screen-triage/licenses/clawbio/LICENSE
skills/crispr-screen-triage/tests/test_crispr_screen_triage.py
skills/crispr-screens-bagel-essentiality/DNAKIT.md
skills/crispr-screens-bagel-essentiality/SKILL.md
skills/crispr-screens-bagel-essentiality/UPSTREAM.md
skills/crispr-screens-bagel-essentiality/usage-guide.md
skills/crispr-screens-bagel-essentiality/examples/run_bagel2.sh
skills/crispr-screens-bagel-essentiality/licenses/bioskills/LICENSE
skills/crispr-screens-base-editing-analysis/DNAKIT.md
skills/crispr-screens-base-editing-analysis/SKILL.md
skills/crispr-screens-base-editing-analysis/UPSTREAM.md
skills/crispr-screens-base-editing-analysis/usage-guide.md
skills/crispr-screens-base-editing-analysis/examples/base_editing_analysis.sh
skills/crispr-screens-base-editing-analysis/licenses/bioskills/LICENSE
skills/crispr-screens-batch-correction/DNAKIT.md
skills/crispr-screens-batch-correction/SKILL.md
skills/crispr-screens-batch-correction/UPSTREAM.md
skills/crispr-screens-batch-correction/usage-guide.md
skills/crispr-screens-batch-correction/examples/batch_correct.py
skills/crispr-screens-batch-correction/licenses/bioskills/LICENSE
skills/crispr-screens-combinatorial-screens/DNAKIT.md
skills/crispr-screens-combinatorial-screens/SKILL.md
skills/crispr-screens-combinatorial-screens/UPSTREAM.md
skills/crispr-screens-combinatorial-screens/usage-guide.md
skills/crispr-screens-combinatorial-screens/examples/gi_scoring.py
skills/crispr-screens-combinatorial-screens/licenses/bioskills/LICENSE
skills/crispr-screens-copy-number-correction/DNAKIT.md
skills/crispr-screens-copy-number-correction/SKILL.md
skills/crispr-screens-copy-number-correction/UPSTREAM.md
skills/crispr-screens-copy-number-correction/usage-guide.md
skills/crispr-screens-copy-number-correction/examples/run_crispr_cleanr.R
skills/crispr-screens-copy-number-correction/licenses/bioskills/LICENSE
skills/crispr-screens-crispresso-editing/DNAKIT.md
skills/crispr-screens-crispresso-editing/SKILL.md
skills/crispr-screens-crispresso-editing/UPSTREAM.md
skills/crispr-screens-crispresso-editing/usage-guide.md
skills/crispr-screens-crispresso-editing/examples/crispresso_analysis.sh
skills/crispr-screens-crispresso-editing/licenses/bioskills/LICENSE
skills/crispr-screens-drugz-chemogenomic/DNAKIT.md
skills/crispr-screens-drugz-chemogenomic/SKILL.md
skills/crispr-screens-drugz-chemogenomic/UPSTREAM.md
skills/crispr-screens-drugz-chemogenomic/usage-guide.md
skills/crispr-screens-drugz-chemogenomic/examples/run_drugz.py
skills/crispr-screens-drugz-chemogenomic/licenses/bioskills/LICENSE
skills/crispr-screens-hit-calling/DNAKIT.md
skills/crispr-screens-hit-calling/SKILL.md
skills/crispr-screens-hit-calling/UPSTREAM.md
skills/crispr-screens-hit-calling/usage-guide.md
skills/crispr-screens-hit-calling/examples/consensus_hits.py
skills/crispr-screens-hit-calling/licenses/bioskills/LICENSE
skills/crispr-screens-in-vivo-screens/DNAKIT.md
skills/crispr-screens-in-vivo-screens/SKILL.md
skills/crispr-screens-in-vivo-screens/UPSTREAM.md
skills/crispr-screens-in-vivo-screens/usage-guide.md
skills/crispr-screens-in-vivo-screens/examples/per_animal_meta_analysis.py
skills/crispr-screens-in-vivo-screens/licenses/bioskills/LICENSE
skills/crispr-screens-jacks-analysis/DNAKIT.md
skills/crispr-screens-jacks-analysis/SKILL.md
skills/crispr-screens-jacks-analysis/UPSTREAM.md
skills/crispr-screens-jacks-analysis/usage-guide.md
skills/crispr-screens-jacks-analysis/examples/run_jacks.py
skills/crispr-screens-jacks-analysis/licenses/bioskills/LICENSE
skills/crispr-screens-library-design/DNAKIT.md
skills/crispr-screens-library-design/SKILL.md
skills/crispr-screens-library-design/UPSTREAM.md
skills/crispr-screens-library-design/usage-guide.md
skills/crispr-screens-library-design/examples/design_library.py
skills/crispr-screens-library-design/licenses/bioskills/LICENSE
skills/crispr-screens-mageck-analysis/DNAKIT.md
skills/crispr-screens-mageck-analysis/SKILL.md
skills/crispr-screens-mageck-analysis/UPSTREAM.md
skills/crispr-screens-mageck-analysis/usage-guide.md
skills/crispr-screens-mageck-analysis/examples/mageck_workflow.sh
skills/crispr-screens-mageck-analysis/licenses/bioskills/LICENSE
skills/crispr-screens-perturb-seq-analysis/DNAKIT.md
skills/crispr-screens-perturb-seq-analysis/SKILL.md
skills/crispr-screens-perturb-seq-analysis/UPSTREAM.md
skills/crispr-screens-perturb-seq-analysis/usage-guide.md
skills/crispr-screens-perturb-seq-analysis/examples/run_pertpy.py
skills/crispr-screens-perturb-seq-analysis/licenses/bioskills/LICENSE
skills/crispr-screens-prime-editing-screens/DNAKIT.md
skills/crispr-screens-prime-editing-screens/SKILL.md
skills/crispr-screens-prime-editing-screens/UPSTREAM.md
skills/crispr-screens-prime-editing-screens/usage-guide.md
skills/crispr-screens-prime-editing-screens/examples/design_pegrna_pridict2.py
skills/crispr-screens-prime-editing-screens/licenses/bioskills/LICENSE
skills/crispr-screens-screen-qc/DNAKIT.md
skills/crispr-screens-screen-qc/SKILL.md
skills/crispr-screens-screen-qc/UPSTREAM.md
skills/crispr-screens-screen-qc/usage-guide.md
skills/crispr-screens-screen-qc/examples/screen_qc.py
skills/crispr-screens-screen-qc/licenses/bioskills/LICENSE
skills/ctdna-mutation-detection/DNAKIT.md
skills/ctdna-mutation-detection/SKILL.md
skills/ctdna-mutation-detection/UPSTREAM.md
skills/ctdna-mutation-detection/usage-guide.md
skills/ctdna-mutation-detection/examples/detect_ctdna_mutations.py
skills/ctdna-mutation-detection/licenses/bioskills/LICENSE
skills/data-provenance/DNAKIT.md
skills/data-provenance/SKILL.md
skills/data-provenance/UPSTREAM.md
skills/data-provenance/licenses/encode-toolkit/CITATION.cff
skills/data-provenance/licenses/encode-toolkit/LICENSE
skills/data-provenance/references/literature.md
skills/data-visualization-circos-plots/DNAKIT.md
skills/data-visualization-circos-plots/SKILL.md
skills/data-visualization-circos-plots/UPSTREAM.md
skills/data-visualization-circos-plots/usage-guide.md
skills/data-visualization-circos-plots/examples/circos_basic.R
skills/data-visualization-circos-plots/examples/circos_basic.py
skills/data-visualization-circos-plots/licenses/bioskills/LICENSE
skills/data-visualization-genome-tracks/DNAKIT.md
skills/data-visualization-genome-tracks/SKILL.md
skills/data-visualization-genome-tracks/UPSTREAM.md
skills/data-visualization-genome-tracks/usage-guide.md
skills/data-visualization-genome-tracks/examples/tracks.ini
skills/data-visualization-genome-tracks/licenses/bioskills/LICENSE
skills/data-visualization-lollipop-protein-maps/DNAKIT.md
skills/data-visualization-lollipop-protein-maps/SKILL.md
skills/data-visualization-lollipop-protein-maps/UPSTREAM.md
skills/data-visualization-lollipop-protein-maps/usage-guide.md
skills/data-visualization-lollipop-protein-maps/examples/lollipop_phd.R
skills/data-visualization-lollipop-protein-maps/licenses/bioskills/LICENSE
skills/data-visualization-manhattan-qq-locuszoom/DNAKIT.md
skills/data-visualization-manhattan-qq-locuszoom/SKILL.md
skills/data-visualization-manhattan-qq-locuszoom/UPSTREAM.md
skills/data-visualization-manhattan-qq-locuszoom/usage-guide.md
skills/data-visualization-manhattan-qq-locuszoom/examples/manhattan_phd.R
skills/data-visualization-manhattan-qq-locuszoom/licenses/bioskills/LICENSE
skills/data-visualization-oncoprint-mutation-matrices/DNAKIT.md
skills/data-visualization-oncoprint-mutation-matrices/SKILL.md
skills/data-visualization-oncoprint-mutation-matrices/UPSTREAM.md
skills/data-visualization-oncoprint-mutation-matrices/usage-guide.md
skills/data-visualization-oncoprint-mutation-matrices/examples/oncoprint_phd.R
skills/data-visualization-oncoprint-mutation-matrices/licenses/bioskills/LICENSE
skills/data-visualization-sequence-logos/DNAKIT.md
skills/data-visualization-sequence-logos/SKILL.md
skills/data-visualization-sequence-logos/UPSTREAM.md
skills/data-visualization-sequence-logos/usage-guide.md
skills/data-visualization-sequence-logos/examples/seqlogo_phd.R
skills/data-visualization-sequence-logos/licenses/bioskills/LICENSE
skills/dbcan/DNAKIT.md
skills/dbcan/SKILL.md
skills/dbcan/UPSTREAM.md
skills/dbcan/agents/openai.yaml
skills/dbcan/licenses/pku-metagenomics/LICENSE
skills/dbcan/references/upstream-docs/compute-setup.md
skills/dbcan/references/upstream-docs/getting-started.md
skills/dbcan/references/upstream-docs/multi-platform.md
skills/dbcan/references/upstream-docs/public-databases.md
skills/dbcan/references/upstream-docs/references.md
skills/dbcan/references/upstream-docs/skills.md
skills/dbcan/references/upstream-docs/standard-pipeline.md
skills/dbcan/references/upstream-docs/tool-selection.md
skills/dbcan/references/upstream-docs/troubleshooting.md
skills/deeptools-ngs-analysis/DNAKIT.md
skills/deeptools-ngs-analysis/SKILL.md
skills/deeptools-ngs-analysis/UPSTREAM.md
skills/deeptools-ngs-analysis/licenses/kdense/CITATION.cff
skills/deeptools-ngs-analysis/licenses/kdense/LICENSE.md
skills/deeptools-ngs-analysis/licenses/sciagent/CC-BY-4.0.txt
skills/deeptools-ngs-analysis/licenses/sciagent/LICENSE
skills/deeptools-ngs-analysis/licenses/tooluniverse/LICENSE
skills/deepurify/DNAKIT.md
skills/deepurify/SKILL.md
skills/deepurify/UPSTREAM.md
skills/deepurify/licenses/pku-metagenomics/LICENSE
skills/deepurify/references/upstream-docs/compute-setup.md
skills/deepurify/references/upstream-docs/getting-started.md
skills/deepurify/references/upstream-docs/multi-platform.md
skills/deepurify/references/upstream-docs/public-databases.md
skills/deepurify/references/upstream-docs/references.md
skills/deepurify/references/upstream-docs/skills.md
skills/deepurify/references/upstream-docs/standard-pipeline.md
skills/deepurify/references/upstream-docs/tool-selection.md
skills/deepurify/references/upstream-docs/troubleshooting.md
skills/defensefinder/DNAKIT.md
skills/defensefinder/SKILL.md
skills/defensefinder/UPSTREAM.md
skills/defensefinder/agents/openai.yaml
skills/defensefinder/licenses/pku-metagenomics/LICENSE
skills/defensefinder/references/upstream-docs/compute-setup.md
skills/defensefinder/references/upstream-docs/getting-started.md
skills/defensefinder/references/upstream-docs/multi-platform.md
skills/defensefinder/references/upstream-docs/public-databases.md
skills/defensefinder/references/upstream-docs/references.md
skills/defensefinder/references/upstream-docs/skills.md
skills/defensefinder/references/upstream-docs/standard-pipeline.md
skills/defensefinder/references/upstream-docs/tool-selection.md
skills/defensefinder/references/upstream-docs/troubleshooting.md
skills/depmap-crispr-essentiality/DNAKIT.md
skills/depmap-crispr-essentiality/SKILL.md
skills/depmap-crispr-essentiality/UPSTREAM.md
skills/depmap-crispr-essentiality/licenses/kdense/CITATION.cff
skills/depmap-crispr-essentiality/licenses/kdense/LICENSE.md
skills/depmap-crispr-essentiality/licenses/sciagent/CC-BY-4.0.txt
skills/depmap-crispr-essentiality/licenses/sciagent/LICENSE
skills/depmap-crispr-essentiality/licenses/tooluniverse/LICENSE
skills/disinfinder/DNAKIT.md
skills/disinfinder/SKILL.md
skills/disinfinder/UPSTREAM.md
skills/disinfinder/licenses/pku-metagenomics/LICENSE
skills/disinfinder/references/upstream-docs/compute-setup.md
skills/disinfinder/references/upstream-docs/getting-started.md
skills/disinfinder/references/upstream-docs/multi-platform.md
skills/disinfinder/references/upstream-docs/public-databases.md
skills/disinfinder/references/upstream-docs/references.md
skills/disinfinder/references/upstream-docs/skills.md
skills/disinfinder/references/upstream-docs/standard-pipeline.md
skills/disinfinder/references/upstream-docs/tool-selection.md
skills/disinfinder/references/upstream-docs/troubleshooting.md
skills/dnabert2/DNAKIT.md
skills/dnabert2/SKILL.md
skills/dnabert2/UPSTREAM.md
skills/dnabert2/licenses/pku-metagenomics/LICENSE
skills/dnabert2/references/upstream-docs/compute-setup.md
skills/dnabert2/references/upstream-docs/getting-started.md
skills/dnabert2/references/upstream-docs/multi-platform.md
skills/dnabert2/references/upstream-docs/public-databases.md
skills/dnabert2/references/upstream-docs/references.md
skills/dnabert2/references/upstream-docs/skills.md
skills/dnabert2/references/upstream-docs/standard-pipeline.md
skills/dnabert2/references/upstream-docs/tool-selection.md
skills/dnabert2/references/upstream-docs/troubleshooting.md
skills/dnakit/DNAKIT.md
skills/dnakit/LICENSE
skills/dnakit/SKILL.md
skills/dnakit/UPSTREAM.md
skills/dnakit-dna-nanotechnology/DNAKIT.md
skills/dnakit-dna-nanotechnology/LICENSE
skills/dnakit-dna-nanotechnology/SKILL.md
skills/dnakit-dna-nanotechnology/UPSTREAM.md
skills/dnakit-dna-storage/DNAKIT.md
skills/dnakit-dna-storage/LICENSE
skills/dnakit-dna-storage/SKILL.md
skills/dnakit-dna-storage/UPSTREAM.md
skills/dnakit-external-genomics/DNAKIT.md
skills/dnakit-external-genomics/LICENSE
skills/dnakit-external-genomics/SKILL.md
skills/dnakit-external-genomics/UPSTREAM.md
skills/dnakit-genomic-breeding/DNAKIT.md
skills/dnakit-genomic-breeding/LICENSE
skills/dnakit-genomic-breeding/SKILL.md
skills/dnakit-genomic-breeding/UPSTREAM.md
skills/dnakit-methylation-summary/DNAKIT.md
skills/dnakit-methylation-summary/LICENSE
skills/dnakit-methylation-summary/SKILL.md
skills/dnakit-methylation-summary/UPSTREAM.md
skills/dnakit-plan/DNAKIT.md
skills/dnakit-plan/LICENSE
skills/dnakit-plan/SKILL.md
skills/dnakit-plan/UPSTREAM.md
skills/dnakit-prokaryotic-genes/DNAKIT.md
skills/dnakit-prokaryotic-genes/LICENSE
skills/dnakit-prokaryotic-genes/SKILL.md
skills/dnakit-prokaryotic-genes/UPSTREAM.md
skills/dnakit/agents/openai.yaml
skills/dnanexus-integration/DNAKIT.md
skills/dnanexus-integration/SKILL.md
skills/dnanexus-integration/UPSTREAM.md
skills/dnanexus-integration/licenses/kdense/CITATION.cff
skills/dnanexus-integration/licenses/kdense/LICENSE.md
skills/dnanexus-integration/references/app-development.md
skills/dnanexus-integration/references/authentication.md
skills/dnanexus-integration/references/configuration.md
skills/dnanexus-integration/references/data-operations.md
skills/dnanexus-integration/references/job-execution.md
skills/dnanexus-integration/references/operations-and-troubleshooting.md
skills/dnanexus-integration/references/python-sdk.md
skills/dnanexus-integration/references/sources.md
skills/dnanexus-integration/references/workflow-languages.md
skills/dnanexus-integration/scripts/inspect_dxpy.py
skills/dnanexus-integration/scripts/validate_dxapp.py
skills/dom-biosurfactant/DNAKIT.md
skills/dom-biosurfactant/SKILL.md
skills/dom-biosurfactant/UPSTREAM.md
skills/dom-biosurfactant/licenses/pku-metagenomics/LICENSE
skills/dom-biosurfactant/references/upstream-docs/compute-setup.md
skills/dom-biosurfactant/references/upstream-docs/getting-started.md
skills/dom-biosurfactant/references/upstream-docs/multi-platform.md
skills/dom-biosurfactant/references/upstream-docs/public-databases.md
skills/dom-biosurfactant/references/upstream-docs/references.md
skills/dom-biosurfactant/references/upstream-docs/skills.md
skills/dom-biosurfactant/references/upstream-docs/standard-pipeline.md
skills/dom-biosurfactant/references/upstream-docs/tool-selection.md
skills/dom-biosurfactant/references/upstream-docs/troubleshooting.md
skills/draft-counseling-summary/DNAKIT.md
skills/draft-counseling-summary/SKILL.md
skills/draft-counseling-summary/UPSTREAM.md
skills/draft-counseling-summary/agents/openai.yaml
skills/draft-counseling-summary/assets/counseling-summary-template.md
skills/draft-counseling-summary/licenses/genetic-counseling/LICENSE
skills/draft-counseling-summary/references/counseling-language.md
skills/dram/DNAKIT.md
skills/dram/SKILL.md
skills/dram/UPSTREAM.md
skills/dram/agents/openai.yaml
skills/dram/licenses/pku-metagenomics/LICENSE
skills/dram/references/upstream-docs/compute-setup.md
skills/dram/references/upstream-docs/getting-started.md
skills/dram/references/upstream-docs/multi-platform.md
skills/dram/references/upstream-docs/public-databases.md
skills/dram/references/upstream-docs/references.md
skills/dram/references/upstream-docs/skills.md
skills/dram/references/upstream-docs/standard-pipeline.md
skills/dram/references/upstream-docs/tool-selection.md
skills/dram/references/upstream-docs/troubleshooting.md
skills/draw-pedigree/DNAKIT.md
skills/draw-pedigree/SKILL.md
skills/draw-pedigree/UPSTREAM.md
skills/draw-pedigree/agents/openai.yaml
skills/draw-pedigree/assets/THIRD_PARTY_NOTICES.md
skills/draw-pedigree/assets/pedigree-chart.html
skills/draw-pedigree/licenses/genetic-counseling/LICENSE
skills/draw-pedigree/references/browser-render.md
skills/draw-pedigree/references/data-formats.md
skills/draw-pedigree/scripts/validate_ped.py
skills/duplicate-handling/DNAKIT.md
skills/duplicate-handling/SKILL.md
skills/duplicate-handling/UPSTREAM.md
skills/duplicate-handling/usage-guide.md
skills/duplicate-handling/examples/markdup_pipeline.sh
skills/duplicate-handling/licenses/bioskills/LICENSE
skills/ecological-genomics-biodiversity-metrics/DNAKIT.md
skills/ecological-genomics-biodiversity-metrics/SKILL.md
skills/ecological-genomics-biodiversity-metrics/UPSTREAM.md
skills/ecological-genomics-biodiversity-metrics/usage-guide.md
skills/ecological-genomics-biodiversity-metrics/examples/beta_partitioning.R
skills/ecological-genomics-biodiversity-metrics/examples/inext_diversity.R
skills/ecological-genomics-biodiversity-metrics/licenses/bioskills/LICENSE
skills/ecological-genomics-community-ecology/DNAKIT.md
skills/ecological-genomics-community-ecology/SKILL.md
skills/ecological-genomics-community-ecology/UPSTREAM.md
skills/ecological-genomics-community-ecology/usage-guide.md
skills/ecological-genomics-community-ecology/examples/constrained_ordination.R
skills/ecological-genomics-community-ecology/examples/indicator_species.R
skills/ecological-genomics-community-ecology/licenses/bioskills/LICENSE
skills/ecological-genomics-conservation-genetics/DNAKIT.md
skills/ecological-genomics-conservation-genetics/SKILL.md
skills/ecological-genomics-conservation-genetics/UPSTREAM.md
skills/ecological-genomics-conservation-genetics/usage-guide.md
skills/ecological-genomics-conservation-genetics/examples/conservation_diversity.R
skills/ecological-genomics-conservation-genetics/examples/ne_estimation.R
skills/ecological-genomics-conservation-genetics/licenses/bioskills/LICENSE
skills/ecological-genomics-edna-metabarcoding/DNAKIT.md
skills/ecological-genomics-edna-metabarcoding/SKILL.md
skills/ecological-genomics-edna-metabarcoding/UPSTREAM.md
skills/ecological-genomics-edna-metabarcoding/usage-guide.md
skills/ecological-genomics-edna-metabarcoding/examples/dada2_edna_coi.R
skills/ecological-genomics-edna-metabarcoding/examples/obitools3_edna_pipeline.sh
skills/ecological-genomics-edna-metabarcoding/licenses/bioskills/LICENSE
skills/ecological-genomics-landscape-genomics/DNAKIT.md
skills/ecological-genomics-landscape-genomics/SKILL.md
skills/ecological-genomics-landscape-genomics/UPSTREAM.md
skills/ecological-genomics-landscape-genomics/usage-guide.md
skills/ecological-genomics-landscape-genomics/examples/lfmm_gea.R
skills/ecological-genomics-landscape-genomics/examples/pcadapt_outliers.R
skills/ecological-genomics-landscape-genomics/licenses/bioskills/LICENSE
skills/ecological-genomics-species-delimitation/DNAKIT.md
skills/ecological-genomics-species-delimitation/SKILL.md
skills/ecological-genomics-species-delimitation/UPSTREAM.md
skills/ecological-genomics-species-delimitation/usage-guide.md
skills/ecological-genomics-species-delimitation/examples/asap_delimitation.py
skills/ecological-genomics-species-delimitation/examples/gmyc_delimitation.R
skills/ecological-genomics-species-delimitation/licenses/bioskills/LICENSE
skills/element-cycling/DNAKIT.md
skills/element-cycling/SKILL.md
skills/element-cycling/UPSTREAM.md
skills/element-cycling/licenses/pku-metagenomics/LICENSE
skills/element-cycling/references/upstream-docs/compute-setup.md
skills/element-cycling/references/upstream-docs/getting-started.md
skills/element-cycling/references/upstream-docs/multi-platform.md
skills/element-cycling/references/upstream-docs/public-databases.md
skills/element-cycling/references/upstream-docs/references.md
skills/element-cycling/references/upstream-docs/skills.md
skills/element-cycling/references/upstream-docs/standard-pipeline.md
skills/element-cycling/references/upstream-docs/tool-selection.md
skills/element-cycling/references/upstream-docs/troubleshooting.md
skills/ena-database/DNAKIT.md
skills/ena-database/SKILL.md
skills/ena-database/UPSTREAM.md
skills/ena-database/licenses/kdense/CITATION.cff
skills/ena-database/licenses/kdense/LICENSE.md
skills/ena-database/licenses/sciagent/CC-BY-4.0.txt
skills/ena-database/licenses/sciagent/LICENSE
skills/ena-database/licenses/tooluniverse/LICENSE
skills/encode-ccres-database/DNAKIT.md
skills/encode-ccres-database/SKILL.md
skills/encode-ccres-database/UPSTREAM.md
skills/encode-ccres-database/licenses/deepmind/CC-BY-4.0.txt
skills/encode-ccres-database/licenses/deepmind/LICENSE
skills/encode-ccres-database/licenses/deepmind/README.md
skills/encode-ccres-database/licenses/deepmind/SKILL_LICENSES.md
skills/encode-ccres-database/references/citation.bib
skills/encode-ccres-database/references/graphql_schema.md
skills/encode-ccres-database/references/json_output_structure.md
skills/encode-ccres-database/scripts/encode_portal_api.py
skills/encode-ccres-database/scripts/screen_api.py
skills/encode-database/DNAKIT.md
skills/encode-database/SKILL.md
skills/encode-database/UPSTREAM.md
skills/encode-database/licenses/kdense/CITATION.cff
skills/encode-database/licenses/kdense/LICENSE.md
skills/encode-database/licenses/sciagent/CC-BY-4.0.txt
skills/encode-database/licenses/sciagent/LICENSE
skills/encode-database/licenses/tooluniverse/LICENSE
skills/encode-toolkit-setup/DNAKIT.md
skills/encode-toolkit-setup/SKILL.md
skills/encode-toolkit-setup/UPSTREAM.md
skills/encode-toolkit-setup/licenses/encode-toolkit/CITATION.cff
skills/encode-toolkit-setup/licenses/encode-toolkit/LICENSE
skills/encode-toolkit-setup/references/literature.md
skills/ensembl-rest/DNAKIT.md
skills/ensembl-rest/SKILL.md
skills/ensembl-rest/UPSTREAM.md
skills/ensembl-rest/usage-guide.md
skills/ensembl-rest/examples/compara_homology.py
skills/ensembl-rest/examples/lookup_and_overlap.py
skills/ensembl-rest/examples/vep_annotation.py
skills/ensembl-rest/licenses/bioskills/LICENSE
skills/entrez-fetch/DNAKIT.md
skills/entrez-fetch/SKILL.md
skills/entrez-fetch/UPSTREAM.md
skills/entrez-fetch/usage-guide.md
skills/entrez-fetch/examples/fetch_pubmed.py
skills/entrez-fetch/examples/fetch_sequences.py
skills/entrez-fetch/examples/fetch_summaries.py
skills/entrez-fetch/licenses/bioskills/LICENSE
skills/entrez-link/DNAKIT.md
skills/entrez-link/SKILL.md
skills/entrez-link/UPSTREAM.md
skills/entrez-link/usage-guide.md
skills/entrez-link/examples/basic_linking.py
skills/entrez-link/examples/chain_links.py
skills/entrez-link/examples/discover_links.py
skills/entrez-link/licenses/bioskills/LICENSE
skills/entrez-search/DNAKIT.md
skills/entrez-search/SKILL.md
skills/entrez-search/UPSTREAM.md
skills/entrez-search/usage-guide.md
skills/entrez-search/examples/basic_search.py
skills/entrez-search/examples/database_info.py
skills/entrez-search/examples/global_query.py
skills/entrez-search/licenses/bioskills/LICENSE
skills/epidemiological-genomics-amr-surveillance/DNAKIT.md
skills/epidemiological-genomics-amr-surveillance/SKILL.md
skills/epidemiological-genomics-amr-surveillance/UPSTREAM.md
skills/epidemiological-genomics-amr-surveillance/usage-guide.md
skills/epidemiological-genomics-amr-surveillance/examples/amr_surveillance.py
skills/epidemiological-genomics-amr-surveillance/licenses/bioskills/LICENSE
skills/epidemiological-genomics-pathogen-typing/DNAKIT.md
skills/epidemiological-genomics-pathogen-typing/SKILL.md
skills/epidemiological-genomics-pathogen-typing/UPSTREAM.md
skills/epidemiological-genomics-pathogen-typing/usage-guide.md
skills/epidemiological-genomics-pathogen-typing/examples/mlst_typing.py
skills/epidemiological-genomics-pathogen-typing/licenses/bioskills/LICENSE
skills/epidemiological-genomics-phylodynamics/DNAKIT.md
skills/epidemiological-genomics-phylodynamics/SKILL.md
skills/epidemiological-genomics-phylodynamics/UPSTREAM.md
skills/epidemiological-genomics-phylodynamics/usage-guide.md
skills/epidemiological-genomics-phylodynamics/examples/treetime_analysis.py
skills/epidemiological-genomics-phylodynamics/licenses/bioskills/LICENSE
skills/epidemiological-genomics-transmission-inference/DNAKIT.md
skills/epidemiological-genomics-transmission-inference/SKILL.md
skills/epidemiological-genomics-transmission-inference/UPSTREAM.md
skills/epidemiological-genomics-transmission-inference/usage-guide.md
skills/epidemiological-genomics-transmission-inference/examples/transmission_inference.py
skills/epidemiological-genomics-transmission-inference/licenses/bioskills/LICENSE
skills/epidemiological-genomics-variant-surveillance/DNAKIT.md
skills/epidemiological-genomics-variant-surveillance/SKILL.md
skills/epidemiological-genomics-variant-surveillance/UPSTREAM.md
skills/epidemiological-genomics-variant-surveillance/usage-guide.md
skills/epidemiological-genomics-variant-surveillance/examples/variant_surveillance.py
skills/epidemiological-genomics-variant-surveillance/licenses/bioskills/LICENSE
skills/epigenomics/.env.template
skills/epigenomics/ANALYSIS_PROCEDURES.md
skills/epigenomics/CODE_REFERENCE.md
skills/epigenomics/DNAKIT.md
skills/epigenomics/QUICK_START.md
skills/epigenomics/SKILL.md
skills/epigenomics/TOOLS_REFERENCE.md
skills/epigenomics/UPSTREAM.md
skills/epigenomics/test_skill.py
skills/epigenomics-chromatin/DNAKIT.md
skills/epigenomics-chromatin/SKILL.md
skills/epigenomics-chromatin/UPSTREAM.md
skills/epigenomics-chromatin/licenses/tooluniverse/LICENSE
skills/epigenomics/licenses/tooluniverse/LICENSE
skills/epigenomics/scripts/methylation_density.py
skills/eqtl-catalogue-region-fetch/.gitignore
skills/eqtl-catalogue-region-fetch/DNAKIT.md
skills/eqtl-catalogue-region-fetch/LICENSE
skills/eqtl-catalogue-region-fetch/SKILL.md
skills/eqtl-catalogue-region-fetch/UPSTREAM.md
skills/eqtl-catalogue-region-fetch/environment.yml
skills/eqtl-catalogue-region-fetch/eqtl_catalogue_region_fetch.py
skills/eqtl-catalogue-region-fetch/examples/default.json
skills/eqtl-catalogue-region-fetch/examples/expected_output.md
skills/eqtl-catalogue-region-fetch/examples/il6r_gtex_small_intestine.json
skills/eqtl-catalogue-region-fetch/examples/input.json
skills/eqtl-catalogue-region-fetch/examples/irf5_gtex_adipose_visceral.json
skills/eqtl-catalogue-region-fetch/examples/run_example.sh
skills/eqtl-catalogue-region-fetch/examples/sort1_gtex_minor_salivary_gland.json
skills/eqtl-catalogue-region-fetch/licenses/clawbio/CITATION.cff
skills/eqtl-catalogue-region-fetch/licenses/clawbio/LICENSE
skills/eqtl-catalogue-region-fetch/tests/__init__.py
skills/eqtl-catalogue-region-fetch/tests/conftest.py
skills/eqtl-catalogue-region-fetch/tests/test_eqtl_catalogue_region_fetch.py
skills/equity-scorer/DNAKIT.md
skills/equity-scorer/SKILL.md
skills/equity-scorer/UPSTREAM.md
skills/equity-scorer/api.py
skills/equity-scorer/equity_scorer.py
skills/equity-scorer/licenses/clawbio/CITATION.cff
skills/equity-scorer/licenses/clawbio/LICENSE
skills/equity-scorer/tests/test_equity_scorer.py
skills/equity-scorer/tests/test_repro_bundle.py
skills/erast/DNAKIT.md
skills/erast/SKILL.md
skills/erast/UPSTREAM.md
skills/erast/licenses/pku-metagenomics/LICENSE
skills/erast/references/upstream-docs/compute-setup.md
skills/erast/references/upstream-docs/getting-started.md
skills/erast/references/upstream-docs/multi-platform.md
skills/erast/references/upstream-docs/public-databases.md
skills/erast/references/upstream-docs/references.md
skills/erast/references/upstream-docs/skills.md
skills/erast/references/upstream-docs/standard-pipeline.md
skills/erast/references/upstream-docs/tool-selection.md
skills/erast/references/upstream-docs/troubleshooting.md
skills/evo2/DNAKIT.md
skills/evo2/SKILL.md
skills/evo2/UPSTREAM.md
skills/evo2-nim/DNAKIT.md
skills/evo2-nim/SKILL.md
skills/evo2-nim/UPSTREAM.md
skills/evo2-nim/config/skillspector-baseline.yml
skills/evo2-nim/evals/config.yml
skills/evo2-nim/evals/evals.json
skills/evo2-nim/evals/trigger_evals.json
skills/evo2-nim/licenses/bionemo/LICENSE
skills/evo2-nim/licenses/bionemo/LICENSE-APACHE-2.0
skills/evo2-nim/licenses/bionemo/LICENSE-CC-BY-4.0
skills/evo2-nim/licenses/bionemo/NOTICE
skills/evo2-nim/references/api.md
skills/evo2-nim/references/examples.md
skills/evo2-nim/references/parameters.md
skills/evo2-nim/references/science.md
skills/evo2-nim/references/validation.md
skills/evo2/licenses/pku-metagenomics/LICENSE
skills/evo2/references/upstream-docs/compute-setup.md
skills/evo2/references/upstream-docs/getting-started.md
skills/evo2/references/upstream-docs/multi-platform.md
skills/evo2/references/upstream-docs/public-databases.md
skills/evo2/references/upstream-docs/references.md
skills/evo2/references/upstream-docs/skills.md
skills/evo2/references/upstream-docs/standard-pipeline.md
skills/evo2/references/upstream-docs/tool-selection.md
skills/evo2/references/upstream-docs/troubleshooting.md
skills/experimental-design-batch-design/DNAKIT.md
skills/experimental-design-batch-design/SKILL.md
skills/experimental-design-batch-design/UPSTREAM.md
skills/experimental-design-batch-design/usage-guide.md
skills/experimental-design-batch-design/examples/batch_design.R
skills/experimental-design-batch-design/licenses/bioskills/LICENSE
skills/experimental-design-multiple-testing/DNAKIT.md
skills/experimental-design-multiple-testing/SKILL.md
skills/experimental-design-multiple-testing/UPSTREAM.md
skills/experimental-design-multiple-testing/usage-guide.md
skills/experimental-design-multiple-testing/examples/multiple_testing_correction.R
skills/experimental-design-multiple-testing/licenses/bioskills/LICENSE
skills/experimental-design-power-analysis/DNAKIT.md
skills/experimental-design-power-analysis/SKILL.md
skills/experimental-design-power-analysis/UPSTREAM.md
skills/experimental-design-power-analysis/usage-guide.md
skills/experimental-design-power-analysis/examples/rnaseq_power.R
skills/experimental-design-power-analysis/licenses/bioskills/LICENSE
skills/experimental-design-randomization-blocking/DNAKIT.md
skills/experimental-design-randomization-blocking/SKILL.md
skills/experimental-design-randomization-blocking/UPSTREAM.md
skills/experimental-design-randomization-blocking/usage-guide.md
skills/experimental-design-randomization-blocking/examples/randomization_blocking.R
skills/experimental-design-randomization-blocking/licenses/bioskills/LICENSE
skills/experimental-design-sample-size/DNAKIT.md
skills/experimental-design-sample-size/SKILL.md
skills/experimental-design-sample-size/UPSTREAM.md
skills/experimental-design-sample-size/usage-guide.md
skills/experimental-design-sample-size/examples/sample_size_estimation.R
skills/experimental-design-sample-size/licenses/bioskills/LICENSE
skills/expression-matrix-gene-id-mapping/DNAKIT.md
skills/expression-matrix-gene-id-mapping/SKILL.md
skills/expression-matrix-gene-id-mapping/UPSTREAM.md
skills/expression-matrix-gene-id-mapping/usage-guide.md
skills/expression-matrix-gene-id-mapping/examples/map_gene_ids.py
skills/expression-matrix-gene-id-mapping/licenses/bioskills/LICENSE
skills/fasta-database-curator/DNAKIT.md
skills/fasta-database-curator/SKILL.md
skills/fasta-database-curator/UPSTREAM.md
skills/fasta-database-curator/tools.md
skills/fasta-database-curator/fixtures/mixed-headers.fasta
skills/fasta-database-curator/licenses/omics/LICENSE
skills/fasta-database-curator/scripts/curate_fasta.py
skills/fastq-quality/DNAKIT.md
skills/fastq-quality/SKILL.md
skills/fastq-quality/UPSTREAM.md
skills/fastq-quality/usage-guide.md
skills/fastq-quality/examples/fastq_quality.py
skills/fastq-quality/licenses/bioskills/LICENSE
skills/fegenie/DNAKIT.md
skills/fegenie/SKILL.md
skills/fegenie/UPSTREAM.md
skills/fegenie/licenses/pku-metagenomics/LICENSE
skills/fegenie/references/upstream-docs/compute-setup.md
skills/fegenie/references/upstream-docs/getting-started.md
skills/fegenie/references/upstream-docs/multi-platform.md
skills/fegenie/references/upstream-docs/public-databases.md
skills/fegenie/references/upstream-docs/references.md
skills/fegenie/references/upstream-docs/skills.md
skills/fegenie/references/upstream-docs/standard-pipeline.md
skills/fegenie/references/upstream-docs/tool-selection.md
skills/fegenie/references/upstream-docs/troubleshooting.md
skills/filter-sequences/DNAKIT.md
skills/filter-sequences/SKILL.md
skills/filter-sequences/UPSTREAM.md
skills/filter-sequences/usage-guide.md
skills/filter-sequences/examples/filter_seqs.py
skills/filter-sequences/licenses/bioskills/LICENSE
skills/find-variant-literature/DNAKIT.md
skills/find-variant-literature/SKILL.md
skills/find-variant-literature/UPSTREAM.md
skills/find-variant-literature/agents/openai.yaml
skills/find-variant-literature/licenses/genetic-counseling/LICENSE
skills/find-variant-literature/references/literature-evidence.md
skills/finemap/DNAKIT.md
skills/finemap/LICENSE
skills/finemap/SKILL.md
skills/finemap/UPSTREAM.md
skills/finemap/references/EXAMPLES.md
skills/finemap/references/LD_OPTIONS.md
skills/finemap/references/SUMMARY_STATS.md
skills/finemap/references/upstream-readme.md
skills/finemap/references/variant-annotate/SKILL.md
skills/finemap/references/variant-annotate/scripts/annotate.py
skills/finemap/scripts/finemap.py
skills/folklore-variant-evidence/DNAKIT.md
skills/folklore-variant-evidence/SKILL.md
skills/folklore-variant-evidence/UPSTREAM.md
skills/folklore-variant-evidence/licenses/kdense/CITATION.cff
skills/folklore-variant-evidence/licenses/kdense/LICENSE.md
skills/folklore-variant-evidence/references/mcp-contract.md
skills/format-conversion/DNAKIT.md
skills/format-conversion/SKILL.md
skills/format-conversion/UPSTREAM.md
skills/format-conversion/usage-guide.md
skills/format-conversion/examples/convert_format.py
skills/format-conversion/licenses/bioskills/LICENSE
skills/foundation-housekeeping/DNAKIT.md
skills/foundation-housekeeping/SKILL.md
skills/foundation-housekeeping/UPSTREAM.md
skills/foundation-housekeeping/docs/README.md
skills/foundation-housekeeping/docs/duckdb.md
skills/foundation-housekeeping/docs/linkml.md
skills/foundation-housekeeping/docs/pixi.md
skills/foundation-housekeeping/docs/pydantic.md
skills/foundation-housekeeping/fixtures/invalid-foreign-keys.json
skills/foundation-housekeeping/fixtures/invalid-project-metadata.json
skills/foundation-housekeeping/fixtures/invalid-provenance-cardinality.json
skills/foundation-housekeeping/fixtures/invalid-result-relations.json
skills/foundation-housekeeping/fixtures/invalid-samples.jsonl
skills/foundation-housekeeping/fixtures/schema-extension-breaking.yaml
skills/foundation-housekeeping/fixtures/schema-extension-compatible.yaml
skills/foundation-housekeeping/fixtures/schema-migration-v1-to-v1.1.json
skills/foundation-housekeeping/fixtures/valid-project-metadata.json
skills/foundation-housekeeping/fixtures/valid-samples.jsonl
skills/foundation-housekeeping/licenses/omics/LICENSE
skills/foundation-housekeeping/schemas/project-metadata.yaml
skills/foundation-housekeeping/scripts/build_metadata_catalog.py
skills/foundation-housekeeping/scripts/build_sample_catalog.py
skills/foundation-housekeeping/scripts/check_schema_compatibility.py
skills/foundation-housekeeping/scripts/generate_models.py
skills/fragment-analysis/DNAKIT.md
skills/fragment-analysis/SKILL.md
skills/fragment-analysis/UPSTREAM.md
skills/fragment-analysis/usage-guide.md
skills/fragment-analysis/examples/fragment_analysis.py
skills/fragment-analysis/licenses/bioskills/LICENSE
skills/functional-genomics-screens/DNAKIT.md
skills/functional-genomics-screens/SKILL.md
skills/functional-genomics-screens/UPSTREAM.md
skills/functional-genomics-screens/licenses/tooluniverse/LICENSE
skills/functional-screen-analysis/DNAKIT.md
skills/functional-screen-analysis/SKILL.md
skills/functional-screen-analysis/UPSTREAM.md
skills/functional-screen-analysis/licenses/encode-toolkit/CITATION.cff
skills/functional-screen-analysis/licenses/encode-toolkit/LICENSE
skills/functional-screen-analysis/references/literature.md
skills/galaxy-bioblend/DNAKIT.md
skills/galaxy-bioblend/LICENSE
skills/galaxy-bioblend/SKILL.md
skills/galaxy-bioblend/UPSTREAM.md
skills/galaxy-bioblend/references/upstream-readme.md
skills/galaxy-bioblend/references/original/SECURITY.md
skills/galaxy-bioblend/references/original/galaxy-bioblend.md
skills/galaxy-bioblend/references/original/galaxy.md
skills/galaxy-bioblend/references/original/setup-credentials.sh
skills/galaxy-bridge/DNAKIT.md
skills/galaxy-bridge/LICENSE
skills/galaxy-bridge/SKILL.md
skills/galaxy-bridge/UPSTREAM.md
skills/galaxy-bridge/galaxy_bridge.py
skills/galaxy-bridge/galaxy_catalog.json
skills/galaxy-bridge/generate_curated_skills.py
skills/galaxy-bridge/generate_galaxy_catalog.py
skills/galaxy-bridge/tool_recommender.py
skills/galaxy-bridge/demo/demo_reads.fq
skills/galaxy-bridge/demo/fastqc_demo_output.html
skills/galaxy-bridge/demo/reproducibility/commands.sh
skills/galaxy-bridge/galaxy_skills/INDEX.md
skills/galaxy-bridge/galaxy_skills/add-lofreq-alignment-quality-scores.md
skills/galaxy-bridge/galaxy_skills/add-metadata.md
skills/galaxy-bridge/galaxy_skills/align-sequences.md
skills/galaxy-bridge/galaxy_skills/alleyoop.md
skills/galaxy-bridge/galaxy_skills/augustus.md
skills/galaxy-bridge/galaxy_skills/axtchain.md
skills/galaxy-bridge/galaxy_skills/bakta.md
skills/galaxy-bridge/galaxy_skills/bam-filter.md
skills/galaxy-bridge/galaxy_skills/bamcompare.md
skills/galaxy-bridge/galaxy_skills/bamleftalign.md
skills/galaxy-bridge/galaxy_skills/bandage-image.md
skills/galaxy-bridge/galaxy_skills/bandage-info.md
skills/galaxy-bridge/galaxy_skills/batched-lastz.md
skills/galaxy-bridge/galaxy_skills/bbtools-bbmap.md
skills/galaxy-bridge/galaxy_skills/bcftools-annotate.md
skills/galaxy-bridge/galaxy_skills/bcftools-call.md
skills/galaxy-bridge/galaxy_skills/bcftools-cnv.md
skills/galaxy-bridge/galaxy_skills/bcftools-color-chrs.md
skills/galaxy-bridge/galaxy_skills/bcftools-csq.md
skills/galaxy-bridge/galaxy_skills/bcftools-dosage.md
skills/galaxy-bridge/galaxy_skills/bcftools-filter.md
skills/galaxy-bridge/galaxy_skills/bcftools-frameshifts.md
skills/galaxy-bridge/galaxy_skills/bcftools-query.md
skills/galaxy-bridge/galaxy_skills/bcftools-stats.md
skills/galaxy-bridge/galaxy_skills/bcftools-tag2tag.md
skills/galaxy-bridge/galaxy_skills/bcftools-view.md
skills/galaxy-bridge/galaxy_skills/bionano-hybrid-scaffold.md
skills/galaxy-bridge/galaxy_skills/bowtie2.md
skills/galaxy-bridge/galaxy_skills/bracken.md
skills/galaxy-bridge/galaxy_skills/bwa-mem.md
skills/galaxy-bridge/galaxy_skills/bwa-mem2.md
skills/galaxy-bridge/galaxy_skills/bwa.md
skills/galaxy-bridge/galaxy_skills/bwameth.md
skills/galaxy-bridge/galaxy_skills/calculate-sequence-complexity.md
skills/galaxy-bridge/galaxy_skills/call-variants.md
skills/galaxy-bridge/galaxy_skills/cat-add-names.md
skills/galaxy-bridge/galaxy_skills/cat-bins.md
skills/galaxy-bridge/galaxy_skills/cat-contigs.md
skills/galaxy-bridge/galaxy_skills/cat-prepare.md
skills/galaxy-bridge/galaxy_skills/cat-summarise.md
skills/galaxy-bridge/galaxy_skills/chainprenet.md
skills/galaxy-bridge/galaxy_skills/chainsort.md
skills/galaxy-bridge/galaxy_skills/circos-alignments-to-links.md
skills/galaxy-bridge/galaxy_skills/circos-bigwig-to-scatter.md
skills/galaxy-bridge/galaxy_skills/circos-interval-to-circos-text-labels.md
skills/galaxy-bridge/galaxy_skills/circos-stack-bigwigs-as-histogram.md
skills/galaxy-bridge/galaxy_skills/clair3.md
skills/galaxy-bridge/galaxy_skills/clustalw.md
skills/galaxy-bridge/galaxy_skills/compute-quality-statistics.md
skills/galaxy-bridge/galaxy_skills/convert-merge-randomize.md
skills/galaxy-bridge/galaxy_skills/convert.md
skills/galaxy-bridge/galaxy_skills/count.md
skills/galaxy-bridge/galaxy_skills/create-assemblies-with-unicycler.md
skills/galaxy-bridge/galaxy_skills/cutadapt.md
skills/galaxy-bridge/galaxy_skills/david.md
skills/galaxy-bridge/galaxy_skills/deepvariant.md
skills/galaxy-bridge/galaxy_skills/delta-filter.md
skills/galaxy-bridge/galaxy_skills/deseq2.md
skills/galaxy-bridge/galaxy_skills/dexseq-count.md
skills/galaxy-bridge/galaxy_skills/dexseq.md
skills/galaxy-bridge/galaxy_skills/diamond-makedb.md
skills/galaxy-bridge/galaxy_skills/diamond-view.md
skills/galaxy-bridge/galaxy_skills/diamond.md
skills/galaxy-bridge/galaxy_skills/diffbind.md
skills/galaxy-bridge/galaxy_skills/dnadiff.md
skills/galaxy-bridge/galaxy_skills/draw-nucleotides-distribution-chart.md
skills/galaxy-bridge/galaxy_skills/draw-quality-score-boxplot.md
skills/galaxy-bridge/galaxy_skills/edger.md
skills/galaxy-bridge/galaxy_skills/extract-maf-blocks.md
skills/galaxy-bridge/galaxy_skills/falco.md
skills/galaxy-bridge/galaxy_skills/fasplit.md
skills/galaxy-bridge/galaxy_skills/fasta-statistics.md
skills/galaxy-bridge/galaxy_skills/fastp.md
skills/galaxy-bridge/galaxy_skills/fastq-info.md
skills/galaxy-bridge/galaxy_skills/fastq-summary-statistics.md
skills/galaxy-bridge/galaxy_skills/fastqc.md
skills/galaxy-bridge/galaxy_skills/fastqe.md
skills/galaxy-bridge/galaxy_skills/featurecounts.md
skills/galaxy-bridge/galaxy_skills/filtlong.md
skills/galaxy-bridge/galaxy_skills/flye-assembly.md
skills/galaxy-bridge/galaxy_skills/freebayes.md
skills/galaxy-bridge/galaxy_skills/g-profiler.md
skills/galaxy-bridge/galaxy_skills/gatk4-mutect2.md
skills/galaxy-bridge/galaxy_skills/gene-length-and-gc-content.md
skills/galaxy-bridge/galaxy_skills/generate-gene-to-transcript-map.md
skills/galaxy-bridge/galaxy_skills/gpass.md
skills/galaxy-bridge/galaxy_skills/hifiasm.md
skills/galaxy-bridge/galaxy_skills/hisat2.md
skills/galaxy-bridge/galaxy_skills/htseq-count.md
skills/galaxy-bridge/galaxy_skills/humann.md
skills/galaxy-bridge/galaxy_skills/insert-indel-qualities.md
skills/galaxy-bridge/galaxy_skills/iq-tree.md
skills/galaxy-bridge/galaxy_skills/jasminesv.md
skills/galaxy-bridge/galaxy_skills/kc-align.md
skills/galaxy-bridge/galaxy_skills/kraken-taxonomic-report.md
skills/galaxy-bridge/galaxy_skills/kraken2.md
skills/galaxy-bridge/galaxy_skills/lastz-d.md
skills/galaxy-bridge/galaxy_skills/lastz.md
skills/galaxy-bridge/galaxy_skills/ld.md
skills/galaxy-bridge/galaxy_skills/limma.md
skills/galaxy-bridge/galaxy_skills/macs2-bdgpeakcall.md
skills/galaxy-bridge/galaxy_skills/macs2-callpeak.md
skills/galaxy-bridge/galaxy_skills/macs2-predictd.md
skills/galaxy-bridge/galaxy_skills/maf-coverage-stats.md
skills/galaxy-bridge/galaxy_skills/mafft-add.md
skills/galaxy-bridge/galaxy_skills/mafft.md
skills/galaxy-bridge/galaxy_skills/maker.md
skills/galaxy-bridge/galaxy_skills/manipulate-fastq.md
skills/galaxy-bridge/galaxy_skills/map-with-minimap2.md
skills/galaxy-bridge/galaxy_skills/masigpro.md
skills/galaxy-bridge/galaxy_skills/maxquant.md
skills/galaxy-bridge/galaxy_skills/medaka-consensus-pipeline.md
skills/galaxy-bridge/galaxy_skills/medaka-consensus-tool.md
skills/galaxy-bridge/galaxy_skills/medaka-variant-pipeline.md
skills/galaxy-bridge/galaxy_skills/medaka-variant-tool.md
skills/galaxy-bridge/galaxy_skills/megahit.md
skills/galaxy-bridge/galaxy_skills/metaphlan.md
skills/galaxy-bridge/galaxy_skills/methyldackel.md
skills/galaxy-bridge/galaxy_skills/metilene.md
skills/galaxy-bridge/galaxy_skills/miniasm.md
skills/galaxy-bridge/galaxy_skills/mirdeep2-mapper.md
skills/galaxy-bridge/galaxy_skills/mirdeep2-quantifier.md
skills/galaxy-bridge/galaxy_skills/mirdeep2.md
skills/galaxy-bridge/galaxy_skills/multiqc.md
skills/galaxy-bridge/galaxy_skills/mummer.md
skills/galaxy-bridge/galaxy_skills/mummerplot.md
skills/galaxy-bridge/galaxy_skills/nanoplot.md
skills/galaxy-bridge/galaxy_skills/nonpareil.md
skills/galaxy-bridge/galaxy_skills/nucmer.md
skills/galaxy-bridge/galaxy_skills/pass.md
skills/galaxy-bridge/galaxy_skills/perform-affine-image-registration-landmark-based.md
skills/galaxy-bridge/galaxy_skills/phyogenetic-reconstruction-with-raxml.md
skills/galaxy-bridge/galaxy_skills/plasflow.md
skills/galaxy-bridge/galaxy_skills/plink.md
skills/galaxy-bridge/galaxy_skills/plotprofile.md
skills/galaxy-bridge/galaxy_skills/porechop.md
skills/galaxy-bridge/galaxy_skills/pretext-snapshot.md
skills/galaxy-bridge/galaxy_skills/pretextmap.md
skills/galaxy-bridge/galaxy_skills/prinseq.md
skills/galaxy-bridge/galaxy_skills/prokka.md
skills/galaxy-bridge/galaxy_skills/purge-overlaps.md
skills/galaxy-bridge/galaxy_skills/pycoqc.md
skills/galaxy-bridge/galaxy_skills/quast.md
skills/galaxy-bridge/galaxy_skills/racon.md
skills/galaxy-bridge/galaxy_skills/rdeval.md
skills/galaxy-bridge/galaxy_skills/rna-starsolo.md
skills/galaxy-bridge/galaxy_skills/rnaspades.md
skills/galaxy-bridge/galaxy_skills/salmon-quant.md
skills/galaxy-bridge/galaxy_skills/salsa.md
skills/galaxy-bridge/galaxy_skills/samtools-ampliconclip.md
skills/galaxy-bridge/galaxy_skills/samtools-depth.md
skills/galaxy-bridge/galaxy_skills/samtools-fastx.md
skills/galaxy-bridge/galaxy_skills/samtools-fixmate.md
skills/galaxy-bridge/galaxy_skills/samtools-flagstat.md
skills/galaxy-bridge/galaxy_skills/samtools-markdup.md
skills/galaxy-bridge/galaxy_skills/samtools-merge.md
skills/galaxy-bridge/galaxy_skills/samtools-mpileup.md
skills/galaxy-bridge/galaxy_skills/samtools-sort.md
skills/galaxy-bridge/galaxy_skills/samtools-view.md
skills/galaxy-bridge/galaxy_skills/seacr.md
skills/galaxy-bridge/galaxy_skills/segalign.md
skills/galaxy-bridge/galaxy_skills/seurat.md
skills/galaxy-bridge/galaxy_skills/shovill.md
skills/galaxy-bridge/galaxy_skills/show-coords.md
skills/galaxy-bridge/galaxy_skills/slamdunk.md
skills/galaxy-bridge/galaxy_skills/sniffles.md
skills/galaxy-bridge/galaxy_skills/snpeff-build.md
skills/galaxy-bridge/galaxy_skills/snpeff-chromosome-info.md
skills/galaxy-bridge/galaxy_skills/snpeff-databases.md
skills/galaxy-bridge/galaxy_skills/snpeff-download.md
skills/galaxy-bridge/galaxy_skills/snpeff-eff.md
skills/galaxy-bridge/galaxy_skills/spades.md
skills/galaxy-bridge/galaxy_skills/strelka-germline.md
skills/galaxy-bridge/galaxy_skills/strelka-somatic.md
skills/galaxy-bridge/galaxy_skills/stringtie-merge.md
skills/galaxy-bridge/galaxy_skills/stringtie.md
skills/galaxy-bridge/galaxy_skills/summary-statistics.md
skills/galaxy-bridge/galaxy_skills/transdecoder.md
skills/galaxy-bridge/galaxy_skills/trim-galore.md
skills/galaxy-bridge/galaxy_skills/trimmomatic.md
skills/galaxy-bridge/galaxy_skills/trinity.md
skills/galaxy-bridge/galaxy_skills/trinotate.md
skills/galaxy-bridge/galaxy_skills/tximport.md
skills/galaxy-bridge/galaxy_skills/umi-tools-count.md
skills/galaxy-bridge/galaxy_skills/umi-tools-deduplicate.md
skills/galaxy-bridge/galaxy_skills/umi-tools-extract.md
skills/galaxy-bridge/galaxy_skills/umi-tools-whitelist.md
skills/galaxy-bridge/galaxy_skills/vcf-to-maf-custom-track.md
skills/galaxy-bridge/galaxy_skills/velvetg.md
skills/galaxy-bridge/galaxy_skills/velveth.md
skills/galaxy-bridge/galaxy_skills/velvetoptimiser.md
skills/galaxy-bridge/galaxy_skills/vsearch-alignment.md
skills/galaxy-bridge/galaxy_skills/vsearch-chimera-detection.md
skills/galaxy-bridge/galaxy_skills/vsearch-clustering.md
skills/galaxy-bridge/galaxy_skills/vsearch-dereplication.md
skills/galaxy-bridge/galaxy_skills/vsearch-masking.md
skills/galaxy-bridge/galaxy_skills/vsearch-search.md
skills/galaxy-bridge/galaxy_skills/vsearch-shuffling.md
skills/galaxy-bridge/galaxy_skills/vsearch-sorting.md
skills/galaxy-bridge/galaxy_skills/winnowmap.md
skills/galaxy-bridge/references/upstream-readme.md
skills/galaxy-bridge/tests/__init__.py
skills/galaxy-bridge/tests/test_galaxy_bridge.py
skills/galaxy-bridge/tests/test_tool_recommender.py
skills/gatk-variant-calling/DNAKIT.md
skills/gatk-variant-calling/SKILL.md
skills/gatk-variant-calling/UPSTREAM.md
skills/gatk-variant-calling/usage-guide.md
skills/gatk-variant-calling/examples/joint_calling.sh
skills/gatk-variant-calling/examples/single_sample.sh
skills/gatk-variant-calling/licenses/bioskills/LICENSE
skills/gene-database/DNAKIT.md
skills/gene-database/SKILL.md
skills/gene-database/UPSTREAM.md
skills/gene-database/licenses/kdense/CITATION.cff
skills/gene-database/licenses/kdense/LICENSE.md
skills/gene-database/licenses/sciagent/CC-BY-4.0.txt
skills/gene-database/licenses/sciagent/LICENSE
skills/gene-database/licenses/tooluniverse/LICENSE
skills/gene-disease-association/DNAKIT.md
skills/gene-disease-association/SKILL.md
skills/gene-disease-association/UPSTREAM.md
skills/gene-disease-association/licenses/tooluniverse/LICENSE
skills/gene-regulatory-networks/DNAKIT.md
skills/gene-regulatory-networks/SKILL.md
skills/gene-regulatory-networks/UPSTREAM.md
skills/gene-regulatory-networks-multiomics-grn/DNAKIT.md
skills/gene-regulatory-networks-multiomics-grn/SKILL.md
skills/gene-regulatory-networks-multiomics-grn/UPSTREAM.md
skills/gene-regulatory-networks-multiomics-grn/usage-guide.md
skills/gene-regulatory-networks-multiomics-grn/examples/figr_paired.R
skills/gene-regulatory-networks-multiomics-grn/examples/scenicplus_multiome.py
skills/gene-regulatory-networks-multiomics-grn/licenses/bioskills/LICENSE
skills/gene-regulatory-networks-scenic-regulons/DNAKIT.md
skills/gene-regulatory-networks-scenic-regulons/SKILL.md
skills/gene-regulatory-networks-scenic-regulons/UPSTREAM.md
skills/gene-regulatory-networks-scenic-regulons/usage-guide.md
skills/gene-regulatory-networks-scenic-regulons/examples/pyscenic_workflow.py
skills/gene-regulatory-networks-scenic-regulons/examples/scenic_visualization.py
skills/gene-regulatory-networks-scenic-regulons/licenses/bioskills/LICENSE
skills/gene-regulatory-networks/licenses/tooluniverse/LICENSE
skills/geniml/DNAKIT.md
skills/geniml/SKILL.md
skills/geniml/UPSTREAM.md
skills/geniml/licenses/kdense/CITATION.cff
skills/geniml/licenses/kdense/LICENSE.md
skills/geniml/references/bedspace.md
skills/geniml/references/consensus_peaks.md
skills/geniml/references/region2vec.md
skills/geniml/references/scembed.md
skills/geniml/references/utilities.md
skills/geniml/scripts/__init__.py
skills/geniml/scripts/_common.py
skills/geniml/scripts/bed_validator.py
skills/geniml/scripts/consensus_plan.py
skills/geniml/scripts/corpus_auditor.py
skills/geniml/scripts/embedding_plan.py
skills/geniml/scripts/model_artifact_inspector.py
skills/geniml/scripts/tokenizer_compatibility.py
skills/genomad/DNAKIT.md
skills/genomad/SKILL.md
skills/genomad/UPSTREAM.md
skills/genomad/agents/openai.yaml
skills/genomad/licenses/pku-metagenomics/LICENSE
skills/genomad/references/upstream-docs/compute-setup.md
skills/genomad/references/upstream-docs/getting-started.md
skills/genomad/references/upstream-docs/multi-platform.md
skills/genomad/references/upstream-docs/public-databases.md
skills/genomad/references/upstream-docs/references.md
skills/genomad/references/upstream-docs/skills.md
skills/genomad/references/upstream-docs/standard-pipeline.md
skills/genomad/references/upstream-docs/tool-selection.md
skills/genomad/references/upstream-docs/troubleshooting.md
skills/genome-annotation-annotation-qc/DNAKIT.md
skills/genome-annotation-annotation-qc/SKILL.md
skills/genome-annotation-annotation-qc/UPSTREAM.md
skills/genome-annotation-annotation-qc/usage-guide.md
skills/genome-annotation-annotation-qc/examples/busco_genome_vs_proteome.sh
skills/genome-annotation-annotation-qc/examples/gene_set_sanity.py
skills/genome-annotation-annotation-qc/licenses/bioskills/LICENSE
skills/genome-annotation-annotation-transfer/DNAKIT.md
skills/genome-annotation-annotation-transfer/SKILL.md
skills/genome-annotation-annotation-transfer/UPSTREAM.md
skills/genome-annotation-annotation-transfer/usage-guide.md
skills/genome-annotation-annotation-transfer/examples/compare_annotations.py
skills/genome-annotation-annotation-transfer/examples/liftoff_transfer.sh
skills/genome-annotation-annotation-transfer/examples/miniprot_crossspecies.sh
skills/genome-annotation-annotation-transfer/licenses/bioskills/LICENSE
skills/genome-annotation-eukaryotic-gene-prediction/DNAKIT.md
skills/genome-annotation-eukaryotic-gene-prediction/SKILL.md
skills/genome-annotation-eukaryotic-gene-prediction/UPSTREAM.md
skills/genome-annotation-eukaryotic-gene-prediction/usage-guide.md
skills/genome-annotation-eukaryotic-gene-prediction/examples/braker3_pipeline.sh
skills/genome-annotation-eukaryotic-gene-prediction/examples/galba_protein_only.sh
skills/genome-annotation-eukaryotic-gene-prediction/licenses/bioskills/LICENSE
skills/genome-annotation-functional-annotation/DNAKIT.md
skills/genome-annotation-functional-annotation/SKILL.md
skills/genome-annotation-functional-annotation/UPSTREAM.md
skills/genome-annotation-functional-annotation/usage-guide.md
skills/genome-annotation-functional-annotation/examples/functional_annotation.sh
skills/genome-annotation-functional-annotation/examples/merge_annotations.py
skills/genome-annotation-functional-annotation/licenses/bioskills/LICENSE
skills/genome-annotation-ncrna-annotation/DNAKIT.md
skills/genome-annotation-ncrna-annotation/SKILL.md
skills/genome-annotation-ncrna-annotation/UPSTREAM.md
skills/genome-annotation-ncrna-annotation/usage-guide.md
skills/genome-annotation-ncrna-annotation/examples/ncrna_annotation.sh
skills/genome-annotation-ncrna-annotation/examples/parse_ncrna.py
skills/genome-annotation-ncrna-annotation/licenses/bioskills/LICENSE
skills/genome-annotation-prokaryotic-annotation/DNAKIT.md
skills/genome-annotation-prokaryotic-annotation/SKILL.md
skills/genome-annotation-prokaryotic-annotation/UPSTREAM.md
skills/genome-annotation-prokaryotic-annotation/usage-guide.md
skills/genome-annotation-prokaryotic-annotation/examples/bakta_annotation.sh
skills/genome-annotation-prokaryotic-annotation/examples/parse_annotation.py
skills/genome-annotation-prokaryotic-annotation/licenses/bioskills/LICENSE
skills/genome-annotation-repeat-annotation/DNAKIT.md
skills/genome-annotation-repeat-annotation/SKILL.md
skills/genome-annotation-repeat-annotation/UPSTREAM.md
skills/genome-annotation-repeat-annotation/usage-guide.md
skills/genome-annotation-repeat-annotation/examples/repeat_annotation.sh
skills/genome-annotation-repeat-annotation/examples/repeat_stats.py
skills/genome-annotation-repeat-annotation/examples/te_expression.py
skills/genome-annotation-repeat-annotation/licenses/bioskills/LICENSE
skills/genome-assembly-assembly-polishing/DNAKIT.md
skills/genome-assembly-assembly-polishing/SKILL.md
skills/genome-assembly-assembly-polishing/UPSTREAM.md
skills/genome-assembly-assembly-polishing/usage-guide.md
skills/genome-assembly-assembly-polishing/examples/polish_assembly.sh
skills/genome-assembly-assembly-polishing/licenses/bioskills/LICENSE
skills/genome-assembly-assembly-qc/DNAKIT.md
skills/genome-assembly-assembly-qc/SKILL.md
skills/genome-assembly-assembly-qc/UPSTREAM.md
skills/genome-assembly-assembly-qc/usage-guide.md
skills/genome-assembly-assembly-qc/examples/run_qc.sh
skills/genome-assembly-assembly-qc/examples/summarize_three_axes.py
skills/genome-assembly-assembly-qc/licenses/bioskills/LICENSE
skills/genome-assembly-contamination-detection/DNAKIT.md
skills/genome-assembly-contamination-detection/SKILL.md
skills/genome-assembly-contamination-detection/UPSTREAM.md
skills/genome-assembly-contamination-detection/usage-guide.md
skills/genome-assembly-contamination-detection/examples/fcs_screen.sh
skills/genome-assembly-contamination-detection/examples/mag_qc_pipeline.sh
skills/genome-assembly-contamination-detection/licenses/bioskills/LICENSE
skills/genome-assembly-genome-profiling/DNAKIT.md
skills/genome-assembly-genome-profiling/SKILL.md
skills/genome-assembly-genome-profiling/UPSTREAM.md
skills/genome-assembly-genome-profiling/usage-guide.md
skills/genome-assembly-genome-profiling/examples/profile_genome.sh
skills/genome-assembly-genome-profiling/licenses/bioskills/LICENSE
skills/genome-assembly-hifi-assembly/DNAKIT.md
skills/genome-assembly-hifi-assembly/SKILL.md
skills/genome-assembly-hifi-assembly/UPSTREAM.md
skills/genome-assembly-hifi-assembly/usage-guide.md
skills/genome-assembly-hifi-assembly/examples/hifi_assembly_workflow.sh
skills/genome-assembly-hifi-assembly/licenses/bioskills/LICENSE
skills/genome-assembly-long-read-assembly/DNAKIT.md
skills/genome-assembly-long-read-assembly/SKILL.md
skills/genome-assembly-long-read-assembly/UPSTREAM.md
skills/genome-assembly-long-read-assembly/usage-guide.md
skills/genome-assembly-long-read-assembly/examples/flye_assembly.sh
skills/genome-assembly-long-read-assembly/licenses/bioskills/LICENSE
skills/genome-assembly-metagenome-assembly/DNAKIT.md
skills/genome-assembly-metagenome-assembly/SKILL.md
skills/genome-assembly-metagenome-assembly/UPSTREAM.md
skills/genome-assembly-metagenome-assembly/usage-guide.md
skills/genome-assembly-metagenome-assembly/examples/metagenome_workflow.sh
skills/genome-assembly-metagenome-assembly/licenses/bioskills/LICENSE
skills/genome-assembly-scaffolding/DNAKIT.md
skills/genome-assembly-scaffolding/SKILL.md
skills/genome-assembly-scaffolding/UPSTREAM.md
skills/genome-assembly-scaffolding/usage-guide.md
skills/genome-assembly-scaffolding/examples/yahs_scaffolding.sh
skills/genome-assembly-scaffolding/licenses/bioskills/LICENSE
skills/genome-assembly-short-read-assembly/DNAKIT.md
skills/genome-assembly-short-read-assembly/SKILL.md
skills/genome-assembly-short-read-assembly/UPSTREAM.md
skills/genome-assembly-short-read-assembly/usage-guide.md
skills/genome-assembly-short-read-assembly/examples/bacterial_assembly.sh
skills/genome-assembly-short-read-assembly/licenses/bioskills/LICENSE
skills/genome-engineering-base-editing-design/DNAKIT.md
skills/genome-engineering-base-editing-design/SKILL.md
skills/genome-engineering-base-editing-design/UPSTREAM.md
skills/genome-engineering-base-editing-design/usage-guide.md
skills/genome-engineering-base-editing-design/examples/base_editing_design.py
skills/genome-engineering-base-editing-design/licenses/bioskills/LICENSE
skills/genome-engineering-grna-design/DNAKIT.md
skills/genome-engineering-grna-design/SKILL.md
skills/genome-engineering-grna-design/UPSTREAM.md
skills/genome-engineering-grna-design/usage-guide.md
skills/genome-engineering-grna-design/examples/grna_design.py
skills/genome-engineering-grna-design/licenses/bioskills/LICENSE
skills/genome-engineering-hdr-template-design/DNAKIT.md
skills/genome-engineering-hdr-template-design/SKILL.md
skills/genome-engineering-hdr-template-design/UPSTREAM.md
skills/genome-engineering-hdr-template-design/usage-guide.md
skills/genome-engineering-hdr-template-design/examples/hdr_template_design.py
skills/genome-engineering-hdr-template-design/licenses/bioskills/LICENSE
skills/genome-engineering-off-target-prediction/DNAKIT.md
skills/genome-engineering-off-target-prediction/SKILL.md
skills/genome-engineering-off-target-prediction/UPSTREAM.md
skills/genome-engineering-off-target-prediction/usage-guide.md
skills/genome-engineering-off-target-prediction/examples/off_target_analysis.py
skills/genome-engineering-off-target-prediction/licenses/bioskills/LICENSE
skills/genome-engineering-prime-editing-design/DNAKIT.md
skills/genome-engineering-prime-editing-design/SKILL.md
skills/genome-engineering-prime-editing-design/UPSTREAM.md
skills/genome-engineering-prime-editing-design/usage-guide.md
skills/genome-engineering-prime-editing-design/examples/prime_editing_design.py
skills/genome-engineering-prime-editing-design/licenses/bioskills/LICENSE
skills/genome-intervals-bed-file-basics/DNAKIT.md
skills/genome-intervals-bed-file-basics/SKILL.md
skills/genome-intervals-bed-file-basics/UPSTREAM.md
skills/genome-intervals-bed-file-basics/usage-guide.md
skills/genome-intervals-bed-file-basics/examples/create_bed.py
skills/genome-intervals-bed-file-basics/examples/validate_bed.sh
skills/genome-intervals-bed-file-basics/licenses/bioskills/LICENSE
skills/genome-intervals-bedgraph-handling/DNAKIT.md
skills/genome-intervals-bedgraph-handling/SKILL.md
skills/genome-intervals-bedgraph-handling/UPSTREAM.md
skills/genome-intervals-bedgraph-handling/usage-guide.md
skills/genome-intervals-bedgraph-handling/examples/bam_to_bigwig.sh
skills/genome-intervals-bedgraph-handling/examples/bedgraph_operations.py
skills/genome-intervals-bedgraph-handling/licenses/bioskills/LICENSE
skills/genome-intervals-bigwig-tracks/DNAKIT.md
skills/genome-intervals-bigwig-tracks/SKILL.md
skills/genome-intervals-bigwig-tracks/UPSTREAM.md
skills/genome-intervals-bigwig-tracks/usage-guide.md
skills/genome-intervals-bigwig-tracks/examples/bedgraph_to_bigwig.sh
skills/genome-intervals-bigwig-tracks/examples/pybigwig_demo.py
skills/genome-intervals-bigwig-tracks/licenses/bioskills/LICENSE
skills/genome-intervals-coverage-analysis/DNAKIT.md
skills/genome-intervals-coverage-analysis/SKILL.md
skills/genome-intervals-coverage-analysis/UPSTREAM.md
skills/genome-intervals-coverage-analysis/usage-guide.md
skills/genome-intervals-coverage-analysis/examples/bedgraph_from_bam.sh
skills/genome-intervals-coverage-analysis/examples/coverage_analysis.py
skills/genome-intervals-coverage-analysis/licenses/bioskills/LICENSE
skills/genome-intervals-gtf-gff-handling/DNAKIT.md
skills/genome-intervals-gtf-gff-handling/SKILL.md
skills/genome-intervals-gtf-gff-handling/UPSTREAM.md
skills/genome-intervals-gtf-gff-handling/usage-guide.md
skills/genome-intervals-gtf-gff-handling/examples/gffread_convert.sh
skills/genome-intervals-gtf-gff-handling/examples/parse_gtf.py
skills/genome-intervals-gtf-gff-handling/licenses/bioskills/LICENSE
skills/genome-intervals-interval-arithmetic/DNAKIT.md
skills/genome-intervals-interval-arithmetic/SKILL.md
skills/genome-intervals-interval-arithmetic/UPSTREAM.md
skills/genome-intervals-interval-arithmetic/usage-guide.md
skills/genome-intervals-interval-arithmetic/examples/intersect_examples.sh
skills/genome-intervals-interval-arithmetic/examples/interval_operations.py
skills/genome-intervals-interval-arithmetic/licenses/bioskills/LICENSE
skills/genome-intervals-overlap-significance/DNAKIT.md
skills/genome-intervals-overlap-significance/SKILL.md
skills/genome-intervals-overlap-significance/UPSTREAM.md
skills/genome-intervals-overlap-significance/usage-guide.md
skills/genome-intervals-overlap-significance/examples/permutation_overlap.py
skills/genome-intervals-overlap-significance/examples/regioner_permtest.R
skills/genome-intervals-overlap-significance/examples/shuffle_permutation_test.sh
skills/genome-intervals-overlap-significance/licenses/bioskills/LICENSE
skills/genome-intervals-proximity-operations/DNAKIT.md
skills/genome-intervals-proximity-operations/SKILL.md
skills/genome-intervals-proximity-operations/UPSTREAM.md
skills/genome-intervals-proximity-operations/usage-guide.md
skills/genome-intervals-proximity-operations/examples/create_promoters.sh
skills/genome-intervals-proximity-operations/examples/proximity_analysis.py
skills/genome-intervals-proximity-operations/licenses/bioskills/LICENSE
skills/genome-language-model/DNAKIT.md
skills/genome-language-model/SKILL.md
skills/genome-language-model/UPSTREAM.md
skills/genome-language-model/licenses/pku-metagenomics/LICENSE
skills/genome-language-model/references/upstream-docs/compute-setup.md
skills/genome-language-model/references/upstream-docs/getting-started.md
skills/genome-language-model/references/upstream-docs/multi-platform.md
skills/genome-language-model/references/upstream-docs/public-databases.md
skills/genome-language-model/references/upstream-docs/references.md
skills/genome-language-model/references/upstream-docs/skills.md
skills/genome-language-model/references/upstream-docs/standard-pipeline.md
skills/genome-language-model/references/upstream-docs/tool-selection.md
skills/genome-language-model/references/upstream-docs/troubleshooting.md
skills/genomic-coordinates/DNAKIT.md
skills/genomic-coordinates/SKILL.md
skills/genomic-coordinates/UPSTREAM.md
skills/genomic-coordinates/licenses/kdense/CITATION.cff
skills/genomic-coordinates/licenses/kdense/LICENSE.md
skills/genomic-coordinates/references/format-conventions.md
skills/genomic-coordinates/references/reference-builds.md
skills/genomic-coordinates/references/transcript-coordinates.md
skills/genomic-coordinates/references/variant-representation.md
skills/genomic-coordinates/scripts/_common.py
skills/genomic-coordinates/scripts/audit_intervals.py
skills/genomic-coordinates/scripts/check_contigs.py
skills/genomic-coordinates/scripts/convert_coords.py
skills/genomic-coordinates/scripts/normalize_variant.py
skills/genomic-intelligence/DNAKIT.md
skills/genomic-intelligence/SKILL.md
skills/genomic-intelligence/UPSTREAM.md
skills/genomic-intelligence/licenses/kdense/CITATION.cff
skills/genomic-intelligence/licenses/kdense/LICENSE.md
skills/genomic-intelligence/references/api-and-auth.md
skills/genomic-intelligence/references/mcp.md
skills/genomic-intelligence/references/sequence-acquisition.md
skills/genomic-intelligence/references/tasks.md
skills/genomics-study-design/DNAKIT.md
skills/genomics-study-design/SKILL.md
skills/genomics-study-design/UPSTREAM.md
skills/genomics-study-design/agents/openai.yaml
skills/genomics-study-design/assets/STUDY_CONTRACT.json.template
skills/genomics-study-design/licenses/research-suite/LICENSE
skills/genomics-study-design/licenses/research-suite/NOTICE
skills/genomics-study-design/references/association-and-validation.md
skills/genomics-study-design/references/complex-genome-analysis.md
skills/genomics-study-design/references/reference-and-variant-qc.md
skills/genomics-study-design/references/study-contract-modes.md
skills/genomics-study-design/scripts/validate_study_contract.py
skills/genomics-workflow-acceleration/.skillsource.json
skills/genomics-workflow-acceleration/DNAKIT.md
skills/genomics-workflow-acceleration/SKILL.md
skills/genomics-workflow-acceleration/UPSTREAM.md
skills/genomics-workflow-acceleration/evals/evals.json
skills/genomics-workflow-acceleration/licenses/bionemo/LICENSE
skills/genomics-workflow-acceleration/licenses/bionemo/LICENSE-APACHE-2.0
skills/genomics-workflow-acceleration/licenses/bionemo/LICENSE-CC-BY-4.0
skills/genomics-workflow-acceleration/licenses/bionemo/NOTICE
skills/genomics-workflow-acceleration/references/comparison-checklist.md
skills/genomics-workflow-acceleration/references/nf-core-parabricks-map.md
skills/genomics-workflow-acceleration/references/parabricks-runtime-readiness.md
skills/genomics-workflow-acceleration/references/parabricks-tool-map.md
skills/genomics-workflow-acceleration/references/step-consolidation.md
skills/genomics-workflow-acceleration/references/workflow-frameworks.md
skills/genomics-workflow-acceleration/references/workflow-layout.md
skills/genotype-imputation-benchmarking/DNAKIT.md
skills/genotype-imputation-benchmarking/SKILL.md
skills/genotype-imputation-benchmarking/UPSTREAM.md
skills/genotype-imputation-benchmarking/agents/openai.yaml
skills/genotype-imputation-benchmarking/assets/BENCHMARK_CONTRACT.json.template
skills/genotype-imputation-benchmarking/assets/BENCHMARK_CONTRACT.schema.json
skills/genotype-imputation-benchmarking/licenses/research-suite/LICENSE
skills/genotype-imputation-benchmarking/licenses/research-suite/NOTICE
skills/genotype-imputation-benchmarking/references/accuracy-metrics.md
skills/genotype-imputation-benchmarking/references/benchmark-design.md
skills/genotype-imputation-benchmarking/references/downstream-and-ensemble-validation.md
skills/genotype-imputation-benchmarking/references/tool-interface-contracts.md
skills/genotype-imputation-benchmarking/scripts/validate_benchmark_contract.py
skills/geo-data/DNAKIT.md
skills/geo-data/SKILL.md
skills/geo-data/UPSTREAM.md
skills/geo-data/usage-guide.md
skills/geo-data/examples/geo_from_pubmed.py
skills/geo-data/examples/geo_to_sra.py
skills/geo-data/examples/search_geo.py
skills/geo-data/licenses/bioskills/LICENSE
skills/gget-genomic-databases/DNAKIT.md
skills/gget-genomic-databases/SKILL.md
skills/gget-genomic-databases/UPSTREAM.md
skills/gget-genomic-databases/licenses/kdense/CITATION.cff
skills/gget-genomic-databases/licenses/kdense/LICENSE.md
skills/gget-genomic-databases/licenses/sciagent/CC-BY-4.0.txt
skills/gget-genomic-databases/licenses/sciagent/LICENSE
skills/gget-genomic-databases/licenses/tooluniverse/LICENSE
skills/gget-genomic-databases/references/databases_workflows.md
skills/gget-genomic-databases/references/module_parameters.md
skills/gigwa-diversity-report/DNAKIT.md
skills/gigwa-diversity-report/LICENSE
skills/gigwa-diversity-report/NOTICE
skills/gigwa-diversity-report/SKILL.md
skills/gigwa-diversity-report/UPSTREAM.md
skills/gigwa-diversity-report/references/popgen-metrics.md
skills/gigwa-diversity-report/references/upstream-readme.md
skills/gigwa-explore-instance/DNAKIT.md
skills/gigwa-explore-instance/LICENSE
skills/gigwa-explore-instance/NOTICE
skills/gigwa-explore-instance/SKILL.md
skills/gigwa-explore-instance/UPSTREAM.md
skills/gigwa-explore-instance/references/instance-anatomy.md
skills/gigwa-explore-instance/references/upstream-readme.md
skills/gigwa-import-and-qc/DNAKIT.md
skills/gigwa-import-and-qc/LICENSE
skills/gigwa-import-and-qc/NOTICE
skills/gigwa-import-and-qc/SKILL.md
skills/gigwa-import-and-qc/UPSTREAM.md
skills/gigwa-import-and-qc/references/import-and-qc.md
skills/gigwa-import-and-qc/references/upstream-readme.md
skills/gigwa-qc-triage/DNAKIT.md
skills/gigwa-qc-triage/LICENSE
skills/gigwa-qc-triage/NOTICE
skills/gigwa-qc-triage/SKILL.md
skills/gigwa-qc-triage/UPSTREAM.md
skills/gigwa-qc-triage/references/qc-thresholds.md
skills/gigwa-qc-triage/references/upstream-readme.md
skills/gigwa-region-scan/DNAKIT.md
skills/gigwa-region-scan/LICENSE
skills/gigwa-region-scan/NOTICE
skills/gigwa-region-scan/SKILL.md
skills/gigwa-region-scan/UPSTREAM.md
skills/gigwa-region-scan/references/region-queries.md
skills/gigwa-region-scan/references/upstream-readme.md
skills/grapevine-adna/DNAKIT.md
skills/grapevine-adna/SKILL.md
skills/grapevine-adna/UPSTREAM.md
skills/grapevine-adna/licenses/plant-skills/LICENSE
skills/gtdb/DNAKIT.md
skills/gtdb/SKILL.md
skills/gtdb/UPSTREAM.md
skills/gtdb/agents/openai.yaml
skills/gtdb/licenses/pku-metagenomics/LICENSE
skills/gtdb/references/upstream-docs/compute-setup.md
skills/gtdb/references/upstream-docs/getting-started.md
skills/gtdb/references/upstream-docs/multi-platform.md
skills/gtdb/references/upstream-docs/public-databases.md
skills/gtdb/references/upstream-docs/references.md
skills/gtdb/references/upstream-docs/skills.md
skills/gtdb/references/upstream-docs/standard-pipeline.md
skills/gtdb/references/upstream-docs/tool-selection.md
skills/gtdb/references/upstream-docs/troubleshooting.md
skills/gtex-database/DNAKIT.md
skills/gtex-database/SKILL.md
skills/gtex-database/UPSTREAM.md
skills/gtex-database/licenses/deepmind/CC-BY-4.0.txt
skills/gtex-database/licenses/deepmind/LICENSE
skills/gtex-database/licenses/deepmind/README.md
skills/gtex-database/licenses/deepmind/SKILL_LICENSES.md
skills/gtex-database/references/citation.bib
skills/gtex-database/scripts/gtex_cli.py
skills/gunc/DNAKIT.md
skills/gunc/SKILL.md
skills/gunc/UPSTREAM.md
skills/gunc/agents/openai.yaml
skills/gunc/licenses/pku-metagenomics/LICENSE
skills/gunc/references/upstream-docs/compute-setup.md
skills/gunc/references/upstream-docs/getting-started.md
skills/gunc/references/upstream-docs/multi-platform.md
skills/gunc/references/upstream-docs/public-databases.md
skills/gunc/references/upstream-docs/references.md
skills/gunc/references/upstream-docs/skills.md
skills/gunc/references/upstream-docs/standard-pipeline.md
skills/gunc/references/upstream-docs/tool-selection.md
skills/gunc/references/upstream-docs/troubleshooting.md
skills/gwas-catalog-region-fetch/.gitignore
skills/gwas-catalog-region-fetch/DNAKIT.md
skills/gwas-catalog-region-fetch/LICENSE
skills/gwas-catalog-region-fetch/SKILL.md
skills/gwas-catalog-region-fetch/UPSTREAM.md
skills/gwas-catalog-region-fetch/environment.yml
skills/gwas-catalog-region-fetch/gwas_catalog_region_fetch.py
skills/gwas-catalog-region-fetch/examples/default.json
skills/gwas-catalog-region-fetch/examples/expected_output.md
skills/gwas-catalog-region-fetch/examples/il6r_crp.yaml
skills/gwas-catalog-region-fetch/examples/input.json
skills/gwas-catalog-region-fetch/examples/run_example.sh
skills/gwas-catalog-region-fetch/examples/sort1_cholesterol_vldl.json
skills/gwas-catalog-region-fetch/examples/tcf7l2_hba1c.json
skills/gwas-catalog-region-fetch/licenses/clawbio/CITATION.cff
skills/gwas-catalog-region-fetch/licenses/clawbio/LICENSE
skills/gwas-catalog-region-fetch/tests/__init__.py
skills/gwas-catalog-region-fetch/tests/conftest.py
skills/gwas-catalog-region-fetch/tests/test_gwas_catalog_region_fetch.py
skills/gwas-catalog-region-fetch/tests/test_live_gwas_catalog_region_fetch.py
skills/gwas-database/DNAKIT.md
skills/gwas-database/SKILL.md
skills/gwas-database/UPSTREAM.md
skills/gwas-database/licenses/kdense/CITATION.cff
skills/gwas-database/licenses/kdense/LICENSE.md
skills/gwas-database/licenses/sciagent/CC-BY-4.0.txt
skills/gwas-database/licenses/sciagent/LICENSE
skills/gwas-database/licenses/tooluniverse/LICENSE
skills/gwas-database/references/api_endpoints.md
skills/gwas-drug-discovery/DNAKIT.md
skills/gwas-drug-discovery/EXAMPLES.md
skills/gwas-drug-discovery/PROCEDURES.md
skills/gwas-drug-discovery/QUICK_START.md
skills/gwas-drug-discovery/REFERENCE.md
skills/gwas-drug-discovery/REPORT_TEMPLATE.md
skills/gwas-drug-discovery/SKILL.md
skills/gwas-drug-discovery/UPSTREAM.md
skills/gwas-drug-discovery/python_implementation.py
skills/gwas-drug-discovery/test_gwas_drug_tools.py
skills/gwas-drug-discovery/test_gwas_drug_tools_v2.py
skills/gwas-drug-discovery/licenses/tooluniverse/LICENSE
skills/gwas-fetch/DNAKIT.md
skills/gwas-fetch/LICENSE
skills/gwas-fetch/SKILL.md
skills/gwas-fetch/UPSTREAM.md
skills/gwas-fetch/references/CATALOG_API.md
skills/gwas-fetch/references/upstream-readme.md
skills/gwas-fetch/scripts/gwas_fetch.py
skills/gwas-snp-interpretation/.env.template
skills/gwas-snp-interpretation/DNAKIT.md
skills/gwas-snp-interpretation/FINAL_VERIFICATION.txt
skills/gwas-snp-interpretation/QUICK_START.md
skills/gwas-snp-interpretation/SKILL.md
skills/gwas-snp-interpretation/UPSTREAM.md
skills/gwas-snp-interpretation/python_implementation.py
skills/gwas-snp-interpretation/test_gwas_snp_tools.py
skills/gwas-snp-interpretation/test_gwas_snp_tools_simple.py
skills/gwas-snp-interpretation/test_skill_comprehensive.py
skills/gwas-snp-interpretation/licenses/tooluniverse/LICENSE
skills/gwas-trait-to-gene/.env.template
skills/gwas-trait-to-gene/DNAKIT.md
skills/gwas-trait-to-gene/SKILL.md
skills/gwas-trait-to-gene/UPSTREAM.md
skills/gwas-trait-to-gene/python_implementation.py
skills/gwas-trait-to-gene/test_gwas_tools.py
skills/gwas-trait-to-gene/test_skill_comprehensive.py
skills/gwas-trait-to-gene/licenses/tooluniverse/LICENSE
skills/hadeg/DNAKIT.md
skills/hadeg/SKILL.md
skills/hadeg/UPSTREAM.md
skills/hadeg/licenses/pku-metagenomics/LICENSE
skills/hadeg/references/upstream-docs/compute-setup.md
skills/hadeg/references/upstream-docs/getting-started.md
skills/hadeg/references/upstream-docs/multi-platform.md
skills/hadeg/references/upstream-docs/public-databases.md
skills/hadeg/references/upstream-docs/references.md
skills/hadeg/references/upstream-docs/skills.md
skills/hadeg/references/upstream-docs/standard-pipeline.md
skills/hadeg/references/upstream-docs/tool-selection.md
skills/hadeg/references/upstream-docs/troubleshooting.md
skills/hi-c-analysis-compartment-analysis/DNAKIT.md
skills/hi-c-analysis-compartment-analysis/SKILL.md
skills/hi-c-analysis-compartment-analysis/UPSTREAM.md
skills/hi-c-analysis-compartment-analysis/usage-guide.md
skills/hi-c-analysis-compartment-analysis/examples/call_compartments.py
skills/hi-c-analysis-compartment-analysis/licenses/bioskills/LICENSE
skills/hi-c-analysis-contact-pairs/DNAKIT.md
skills/hi-c-analysis-contact-pairs/SKILL.md
skills/hi-c-analysis-contact-pairs/UPSTREAM.md
skills/hi-c-analysis-contact-pairs/usage-guide.md
skills/hi-c-analysis-contact-pairs/examples/fastq_to_pairs.sh
skills/hi-c-analysis-contact-pairs/licenses/bioskills/LICENSE
skills/hi-c-analysis-hic-data-io/DNAKIT.md
skills/hi-c-analysis-hic-data-io/SKILL.md
skills/hi-c-analysis-hic-data-io/UPSTREAM.md
skills/hi-c-analysis-hic-data-io/usage-guide.md
skills/hi-c-analysis-hic-data-io/examples/load_cooler.py
skills/hi-c-analysis-hic-data-io/licenses/bioskills/LICENSE
skills/hi-c-analysis-hic-differential/DNAKIT.md
skills/hi-c-analysis-hic-differential/SKILL.md
skills/hi-c-analysis-hic-differential/UPSTREAM.md
skills/hi-c-analysis-hic-differential/usage-guide.md
skills/hi-c-analysis-hic-differential/examples/differential_contacts.R
skills/hi-c-analysis-hic-differential/licenses/bioskills/LICENSE
skills/hi-c-analysis-hic-visualization/DNAKIT.md
skills/hi-c-analysis-hic-visualization/SKILL.md
skills/hi-c-analysis-hic-visualization/UPSTREAM.md
skills/hi-c-analysis-hic-visualization/usage-guide.md
skills/hi-c-analysis-hic-visualization/examples/plot_hic.py
skills/hi-c-analysis-hic-visualization/licenses/bioskills/LICENSE
skills/hi-c-analysis-hichip-plac-loops/DNAKIT.md
skills/hi-c-analysis-hichip-plac-loops/SKILL.md
skills/hi-c-analysis-hichip-plac-loops/UPSTREAM.md
skills/hi-c-analysis-hichip-plac-loops/usage-guide.md
skills/hi-c-analysis-hichip-plac-loops/examples/run_fithichip.sh
skills/hi-c-analysis-hichip-plac-loops/licenses/bioskills/LICENSE
skills/hi-c-analysis-loop-calling/DNAKIT.md
skills/hi-c-analysis-loop-calling/SKILL.md
skills/hi-c-analysis-loop-calling/UPSTREAM.md
skills/hi-c-analysis-loop-calling/usage-guide.md
skills/hi-c-analysis-loop-calling/examples/call_loops.py
skills/hi-c-analysis-loop-calling/licenses/bioskills/LICENSE
skills/hi-c-analysis-matrix-operations/DNAKIT.md
skills/hi-c-analysis-matrix-operations/SKILL.md
skills/hi-c-analysis-matrix-operations/UPSTREAM.md
skills/hi-c-analysis-matrix-operations/usage-guide.md
skills/hi-c-analysis-matrix-operations/examples/balance_and_oe.py
skills/hi-c-analysis-matrix-operations/licenses/bioskills/LICENSE
skills/hi-c-analysis-tad-detection/DNAKIT.md
skills/hi-c-analysis-tad-detection/SKILL.md
skills/hi-c-analysis-tad-detection/UPSTREAM.md
skills/hi-c-analysis-tad-detection/usage-guide.md
skills/hi-c-analysis-tad-detection/examples/call_tads.py
skills/hi-c-analysis-tad-detection/licenses/bioskills/LICENSE
skills/hic-aggregation/DNAKIT.md
skills/hic-aggregation/SKILL.md
skills/hic-aggregation/UPSTREAM.md
skills/hic-aggregation/licenses/encode-toolkit/CITATION.cff
skills/hic-aggregation/licenses/encode-toolkit/LICENSE
skills/hic-aggregation/references/literature.md
skills/hic-aggregation/references/loop-caller-comparison.md
skills/hic-aggregation/scripts/validate_loops.py
skills/histone-aggregation/DNAKIT.md
skills/histone-aggregation/SKILL.md
skills/histone-aggregation/UPSTREAM.md
skills/histone-aggregation/licenses/encode-toolkit/CITATION.cff
skills/histone-aggregation/licenses/encode-toolkit/LICENSE
skills/histone-aggregation/references/broad-vs-narrow.md
skills/histone-aggregation/references/histone-marks-reference.md
skills/histone-aggregation/references/literature.md
skills/histone-aggregation/references/signal-filtering.md
skills/histone-aggregation/scripts/validate_peaks.py
skills/hla-immunogenomics/DNAKIT.md
skills/hla-immunogenomics/SKILL.md
skills/hla-immunogenomics/UPSTREAM.md
skills/hla-immunogenomics/licenses/tooluniverse/LICENSE
skills/illumina-bridge/DNAKIT.md
skills/illumina-bridge/SKILL.md
skills/illumina-bridge/UPSTREAM.md
skills/illumina-bridge/illumina_bridge.py
skills/illumina-bridge/illumina_bundle.py
skills/illumina-bridge/illumina_providers.py
skills/illumina-bridge/demo_bundle/SampleSheet.csv
skills/illumina-bridge/demo_bundle/demo.vcf
skills/illumina-bridge/demo_bundle/mock_ica_metadata.json
skills/illumina-bridge/demo_bundle/qc_metrics.json
skills/illumina-bridge/licenses/clawbio/CITATION.cff
skills/illumina-bridge/licenses/clawbio/LICENSE
skills/illumina-bridge/tests/test_illumina_bridge.py
skills/immune-repertoire-analysis/ANALYSIS_DETAILS.md
skills/immune-repertoire-analysis/DNAKIT.md
skills/immune-repertoire-analysis/SKILL.md
skills/immune-repertoire-analysis/UPSTREAM.md
skills/immune-repertoire-analysis/USE_CASES.md
skills/immune-repertoire-analysis/licenses/tooluniverse/LICENSE
skills/immunoinformatics-epitope-prediction/DNAKIT.md
skills/immunoinformatics-epitope-prediction/SKILL.md
skills/immunoinformatics-epitope-prediction/UPSTREAM.md
skills/immunoinformatics-epitope-prediction/usage-guide.md
skills/immunoinformatics-epitope-prediction/examples/epitope_prediction.py
skills/immunoinformatics-epitope-prediction/licenses/bioskills/LICENSE
skills/immunoinformatics-immunogenicity-scoring/DNAKIT.md
skills/immunoinformatics-immunogenicity-scoring/SKILL.md
skills/immunoinformatics-immunogenicity-scoring/UPSTREAM.md
skills/immunoinformatics-immunogenicity-scoring/usage-guide.md
skills/immunoinformatics-immunogenicity-scoring/examples/immunogenicity_scoring.py
skills/immunoinformatics-immunogenicity-scoring/licenses/bioskills/LICENSE
skills/immunoinformatics-mhc-binding-prediction/DNAKIT.md
skills/immunoinformatics-mhc-binding-prediction/SKILL.md
skills/immunoinformatics-mhc-binding-prediction/UPSTREAM.md
skills/immunoinformatics-mhc-binding-prediction/usage-guide.md
skills/immunoinformatics-mhc-binding-prediction/examples/mhc_binding.py
skills/immunoinformatics-mhc-binding-prediction/licenses/bioskills/LICENSE
skills/immunoinformatics-mhc-class-ii-prediction/DNAKIT.md
skills/immunoinformatics-mhc-class-ii-prediction/SKILL.md
skills/immunoinformatics-mhc-class-ii-prediction/UPSTREAM.md
skills/immunoinformatics-mhc-class-ii-prediction/usage-guide.md
skills/immunoinformatics-mhc-class-ii-prediction/examples/class_ii_pairing.py
skills/immunoinformatics-mhc-class-ii-prediction/examples/run_class_ii.sh
skills/immunoinformatics-mhc-class-ii-prediction/licenses/bioskills/LICENSE
skills/immunoinformatics-neoantigen-prediction/DNAKIT.md
skills/immunoinformatics-neoantigen-prediction/SKILL.md
skills/immunoinformatics-neoantigen-prediction/UPSTREAM.md
skills/immunoinformatics-neoantigen-prediction/usage-guide.md
skills/immunoinformatics-neoantigen-prediction/examples/neoantigen_prediction.py
skills/immunoinformatics-neoantigen-prediction/licenses/bioskills/LICENSE
skills/importing-tracks/DNAKIT.md
skills/importing-tracks/SKILL.md
skills/importing-tracks/UPSTREAM.md
skills/importing-tracks/licenses/misha/LICENSE
skills/importing-tracks/licenses/misha/LICENSE.md
skills/insilicoseq/DNAKIT.md
skills/insilicoseq/SKILL.md
skills/insilicoseq/UPSTREAM.md
skills/insilicoseq/licenses/pku-metagenomics/LICENSE
skills/insilicoseq/references/upstream-docs/compute-setup.md
skills/insilicoseq/references/upstream-docs/getting-started.md
skills/insilicoseq/references/upstream-docs/multi-platform.md
skills/insilicoseq/references/upstream-docs/public-databases.md
skills/insilicoseq/references/upstream-docs/references.md
skills/insilicoseq/references/upstream-docs/skills.md
skills/insilicoseq/references/upstream-docs/standard-pipeline.md
skills/insilicoseq/references/upstream-docs/tool-selection.md
skills/insilicoseq/references/upstream-docs/troubleshooting.md
skills/instrument-data-to-allotrope/DNAKIT.md
skills/instrument-data-to-allotrope/LICENSE
skills/instrument-data-to-allotrope/LICENSE.txt
skills/instrument-data-to-allotrope/SKILL.md
skills/instrument-data-to-allotrope/UPSTREAM.md
skills/instrument-data-to-allotrope/requirements.txt
skills/instrument-data-to-allotrope/references/asm_schema_overview.md
skills/instrument-data-to-allotrope/references/field_classification_guide.md
skills/instrument-data-to-allotrope/references/flattening_guide.md
skills/instrument-data-to-allotrope/references/supported_instruments.md
skills/instrument-data-to-allotrope/references/upstream-readme.md
skills/instrument-data-to-allotrope/scripts/convert_to_asm.py
skills/instrument-data-to-allotrope/scripts/export_parser.py
skills/instrument-data-to-allotrope/scripts/flatten_asm.py
skills/instrument-data-to-allotrope/scripts/validate_asm.py
skills/integronfinder/DNAKIT.md
skills/integronfinder/SKILL.md
skills/integronfinder/UPSTREAM.md
skills/integronfinder/licenses/pku-metagenomics/LICENSE
skills/integronfinder/references/upstream-docs/compute-setup.md
skills/integronfinder/references/upstream-docs/getting-started.md
skills/integronfinder/references/upstream-docs/multi-platform.md
skills/integronfinder/references/upstream-docs/public-databases.md
skills/integronfinder/references/upstream-docs/references.md
skills/integronfinder/references/upstream-docs/skills.md
skills/integronfinder/references/upstream-docs/standard-pipeline.md
skills/integronfinder/references/upstream-docs/tool-selection.md
skills/integronfinder/references/upstream-docs/troubleshooting.md
skills/interdomain-hgt/DNAKIT.md
skills/interdomain-hgt/SKILL.md
skills/interdomain-hgt/UPSTREAM.md
skills/interdomain-hgt/docs/README.md
skills/interdomain-hgt/docs/database-availability.md
skills/interdomain-hgt/fixtures/arbiter.dmnd
skills/interdomain-hgt/fixtures/arbiter_hits.tsv
skills/interdomain-hgt/fixtures/comparison.fna
skills/interdomain-hgt/fixtures/context.tsv
skills/interdomain-hgt/fixtures/databases.json
skills/interdomain-hgt/fixtures/forward_hits.tsv
skills/interdomain-hgt/fixtures/hypotheses.tsv
skills/interdomain-hgt/fixtures/labels.tsv
skills/interdomain-hgt/fixtures/reciprocal.tsv
skills/interdomain-hgt/fixtures/reflections.tsv
skills/interdomain-hgt/fixtures/sampling_depth.tsv
skills/interdomain-hgt/fixtures/trees.tsv
skills/interdomain-hgt/licenses/omics/LICENSE
skills/interdomain-hgt/schemas/hgt-evidence.schema.json
skills/interdomain-hgt/scripts/run_hgt_evidence.py
skills/interpret-negative-or-vus/DNAKIT.md
skills/interpret-negative-or-vus/SKILL.md
skills/interpret-negative-or-vus/UPSTREAM.md
skills/interpret-negative-or-vus/agents/openai.yaml
skills/interpret-negative-or-vus/licenses/genetic-counseling/LICENSE
skills/interpret-negative-or-vus/references/assay-blind-spots.md
skills/interpro-database/DNAKIT.md
skills/interpro-database/LICENSE
skills/interpro-database/SKILL.md
skills/interpro-database/SKILL_LICENSES.md
skills/interpro-database/UPSTREAM.md
skills/interpro-database/references/api_reference.md
skills/interpro-database/references/citation.bib
skills/interpro-database/references/example_responses.tsv
skills/interpro-database/references/upstream-readme.md
skills/interpro-database/references/uv/SKILL.md
skills/interpro-database/scripts/interpro_client.py
skills/isabl-debug-analysis/DNAKIT.md
skills/isabl-debug-analysis/SKILL.md
skills/isabl-debug-analysis/UPSTREAM.md
skills/isabl-debug-analysis/licenses/isabl/LICENSE
skills/isabl-merge-results/DNAKIT.md
skills/isabl-merge-results/SKILL.md
skills/isabl-merge-results/UPSTREAM.md
skills/isabl-merge-results/licenses/isabl/LICENSE
skills/isabl-monitor-analyses/DNAKIT.md
skills/isabl-monitor-analyses/SKILL.md
skills/isabl-monitor-analyses/UPSTREAM.md
skills/isabl-monitor-analyses/licenses/isabl/LICENSE
skills/isabl-project-report/DNAKIT.md
skills/isabl-project-report/SKILL.md
skills/isabl-project-report/UPSTREAM.md
skills/isabl-project-report/licenses/isabl/LICENSE
skills/isabl-query-data/DNAKIT.md
skills/isabl-query-data/SKILL.md
skills/isabl-query-data/UPSTREAM.md
skills/isabl-query-data/licenses/isabl/LICENSE
skills/isabl-run-pipeline/DNAKIT.md
skills/isabl-run-pipeline/SKILL.md
skills/isabl-run-pipeline/UPSTREAM.md
skills/isabl-run-pipeline/licenses/isabl/LICENSE
skills/isabl-submit-data/DNAKIT.md
skills/isabl-submit-data/SKILL.md
skills/isabl-submit-data/UPSTREAM.md
skills/isabl-submit-data/licenses/isabl/LICENSE
skills/isabl-write-app/DNAKIT.md
skills/isabl-write-app/SKILL.md
skills/isabl-write-app/UPSTREAM.md
skills/isabl-write-app/licenses/isabl/LICENSE
skills/isescan/DNAKIT.md
skills/isescan/SKILL.md
skills/isescan/UPSTREAM.md
skills/isescan/licenses/pku-metagenomics/LICENSE
skills/isescan/references/upstream-docs/compute-setup.md
skills/isescan/references/upstream-docs/getting-started.md
skills/isescan/references/upstream-docs/multi-platform.md
skills/isescan/references/upstream-docs/public-databases.md
skills/isescan/references/upstream-docs/references.md
skills/isescan/references/upstream-docs/skills.md
skills/isescan/references/upstream-docs/standard-pipeline.md
skills/isescan/references/upstream-docs/tool-selection.md
skills/isescan/references/upstream-docs/troubleshooting.md
skills/jaspar-database/DNAKIT.md
skills/jaspar-database/SKILL.md
skills/jaspar-database/UPSTREAM.md
skills/jaspar-database/licenses/kdense/CITATION.cff
skills/jaspar-database/licenses/kdense/LICENSE.md
skills/jaspar-database/licenses/sciagent/CC-BY-4.0.txt
skills/jaspar-database/licenses/sciagent/LICENSE
skills/jaspar-database/licenses/tooluniverse/LICENSE
skills/kiro-healthomics-genomics/DNAKIT.md
skills/kiro-healthomics-genomics/LICENSE
skills/kiro-healthomics-genomics/SKILL.md
skills/kiro-healthomics-genomics/THIRD-PARTY.txt
skills/kiro-healthomics-genomics/UPSTREAM.md
skills/kiro-healthomics-genomics/references/upstream-readme.md
skills/kiro-healthomics-genomics/references/original/kiro-life-sciences/POWER.md
skills/kiro-healthomics-genomics/references/original/kiro-life-sciences/skills/bioinformatics-file-formats.md
skills/kiro-healthomics-genomics/references/original/kiro-life-sciences/skills/genomics-pipeline-best-practices.md
skills/kiro-healthomics-genomics/references/original/kiro-life-sciences/steering/pipeline-import-healthomics.md
skills/kiro-healthomics-genomics/references/original/kiro-life-sciences/steering/variant-calling-pipeline.md
skills/ld-1000g-region-compute/.gitignore
skills/ld-1000g-region-compute/DNAKIT.md
skills/ld-1000g-region-compute/LICENSE
skills/ld-1000g-region-compute/SKILL.md
skills/ld-1000g-region-compute/UPSTREAM.md
skills/ld-1000g-region-compute/environment.yml
skills/ld-1000g-region-compute/ld_1000g_region_compute.py
skills/ld-1000g-region-compute/ondemand_client.py
skills/ld-1000g-region-compute/examples/default.json
skills/ld-1000g-region-compute/examples/expected_output.md
skills/ld-1000g-region-compute/examples/run_example.sh
skills/ld-1000g-region-compute/examples/sort1_locus_eur.json
skills/ld-1000g-region-compute/licenses/clawbio/CITATION.cff
skills/ld-1000g-region-compute/licenses/clawbio/LICENSE
skills/ld-1000g-region-compute/tests/__init__.py
skills/ld-1000g-region-compute/tests/conftest.py
skills/ld-1000g-region-compute/tests/test_ld_1000g_region_compute.py
skills/ld-1000g-region-compute/tests/test_live_ld_1000g_region_compute.py
skills/ldsc/DNAKIT.md
skills/ldsc/LICENSE
skills/ldsc/SKILL.md
skills/ldsc/UPSTREAM.md
skills/ldsc/references/LDSC_REFS.md
skills/ldsc/references/upstream-readme.md
skills/ldsc/scripts/ldsc.py
skills/lexicmap/DNAKIT.md
skills/lexicmap/SKILL.md
skills/lexicmap/UPSTREAM.md
skills/lexicmap/licenses/pku-metagenomics/LICENSE
skills/lexicmap/references/upstream-docs/compute-setup.md
skills/lexicmap/references/upstream-docs/getting-started.md
skills/lexicmap/references/upstream-docs/multi-platform.md
skills/lexicmap/references/upstream-docs/public-databases.md
skills/lexicmap/references/upstream-docs/references.md
skills/lexicmap/references/upstream-docs/skills.md
skills/lexicmap/references/upstream-docs/standard-pipeline.md
skills/lexicmap/references/upstream-docs/tool-selection.md
skills/lexicmap/references/upstream-docs/troubleshooting.md
skills/liftover/DNAKIT.md
skills/liftover/LICENSE
skills/liftover/SKILL.md
skills/liftover/UPSTREAM.md
skills/liftover-coordinates/DNAKIT.md
skills/liftover-coordinates/SKILL.md
skills/liftover-coordinates/UPSTREAM.md
skills/liftover-coordinates/licenses/encode-toolkit/CITATION.cff
skills/liftover-coordinates/licenses/encode-toolkit/LICENSE
skills/liftover-coordinates/references/literature.md
skills/liftover/references/COVERAGE_GAPS.md
skills/liftover/references/upstream-readme.md
skills/liftover/scripts/lift_sumstats.py
skills/local-blast/DNAKIT.md
skills/local-blast/SKILL.md
skills/local-blast/UPSTREAM.md
skills/local-blast/usage-guide.md
skills/local-blast/examples/blast_wrapper.py
skills/local-blast/examples/create_database.sh
skills/local-blast/examples/reciprocal_best.sh
skills/local-blast/examples/run_blast.sh
skills/local-blast/licenses/bioskills/LICENSE
skills/locuscompare-region-render/.gitignore
skills/locuscompare-region-render/DNAKIT.md
skills/locuscompare-region-render/INPUT_SCHEMA.md
skills/locuscompare-region-render/LICENSE
skills/locuscompare-region-render/SKILL.md
skills/locuscompare-region-render/UPSTREAM.md
skills/locuscompare-region-render/_prefetched.py
skills/locuscompare-region-render/_wald_ratio_types.py
skills/locuscompare-region-render/cli.py
skills/locuscompare-region-render/commands.sh
skills/locuscompare-region-render/environment.yml
skills/locuscompare-region-render/locuscompare_region_render.py
skills/locuscompare-region-render/regional_plot.py
skills/locuscompare-region-render/_fetchers/__init__.py
skills/locuscompare-region-render/_fetchers/gencode_ondemand.py
skills/locuscompare-region-render/examples/README.md
skills/locuscompare-region-render/examples/01_synthetic_demo/README.md
skills/locuscompare-region-render/examples/01_synthetic_demo/config.json
skills/locuscompare-region-render/examples/01_synthetic_demo/exposure.tsv
skills/locuscompare-region-render/examples/01_synthetic_demo/generate_synthetic_fixtures.py
skills/locuscompare-region-render/examples/01_synthetic_demo/genes.tsv
skills/locuscompare-region-render/examples/01_synthetic_demo/ld_matrix.tsv
skills/locuscompare-region-render/examples/01_synthetic_demo/outcome.tsv
skills/locuscompare-region-render/examples/02_eqtl_catalogue_x_gwas_catalog/README.md
skills/locuscompare-region-render/examples/02_eqtl_catalogue_x_gwas_catalog/config.yaml
skills/locuscompare-region-render/examples/03_open_targets_followup/README.md
skills/locuscompare-region-render/examples/03_open_targets_followup/config.yaml
skills/locuscompare-region-render/examples/03_open_targets_followup/ot_row.json
skills/locuscompare-region-render/examples/04_gwas_lookup_followup/README.md
skills/locuscompare-region-render/examples/04_gwas_lookup_followup/config.yaml
skills/locuscompare-region-render/examples/05_sqtl_sort1_liver_txrev/README.md
skills/locuscompare-region-render/examples/05_sqtl_sort1_liver_txrev/config.yaml
skills/locuscompare-region-render/examples/05_sqtl_sort1_liver_txrev/expected_output/1_109274968_G_T_full_locuscompare.png
skills/locuscompare-region-render/examples/05_sqtl_sort1_liver_txrev/expected_output/manifest.yaml
skills/locuscompare-region-render/examples/05_sqtl_sort1_liver_txrev/expected_output/report.md
skills/locuscompare-region-render/examples/06_sceqtl_sort1_onek1k_cd14_mono/README.md
skills/locuscompare-region-render/examples/06_sceqtl_sort1_onek1k_cd14_mono/config.yaml
skills/locuscompare-region-render/examples/06_sceqtl_sort1_onek1k_cd14_mono/expected_output/1_109274968_G_T_full_locuscompare.png
skills/locuscompare-region-render/examples/06_sceqtl_sort1_onek1k_cd14_mono/expected_output/manifest.yaml
skills/locuscompare-region-render/examples/06_sceqtl_sort1_onek1k_cd14_mono/expected_output/report.md
skills/locuscompare-region-render/examples/07_pqtl_sort1_ukbppp_eur/README.md
skills/locuscompare-region-render/examples/07_pqtl_sort1_ukbppp_eur/config.yaml
skills/locuscompare-region-render/examples/07_pqtl_sort1_ukbppp_eur/expected_output/1_109274968_G_T_full_locuscompare.png
skills/locuscompare-region-render/examples/07_pqtl_sort1_ukbppp_eur/expected_output/manifest.yaml
skills/locuscompare-region-render/examples/07_pqtl_sort1_ukbppp_eur/expected_output/report.md
skills/locuscompare-region-render/examples/chains/finemapping_chain/README.md
skills/locuscompare-region-render/examples/chains/finemapping_chain/config.yaml
skills/locuscompare-region-render/examples/recipes/finngen_direct/README.md
skills/locuscompare-region-render/examples/recipes/finngen_direct/harmonise.sh
skills/locuscompare-region-render/examples/recipes/gtex_v10_direct/README.md
skills/locuscompare-region-render/examples/recipes/gtex_v10_direct/harmonise.sh
skills/locuscompare-region-render/examples/recipes/pan_ukbb_direct/README.md
skills/locuscompare-region-render/examples/recipes/pan_ukbb_direct/harmonise.sh
skills/locuscompare-region-render/examples/recipes/ukb_ppp_pqtl/README.md
skills/locuscompare-region-render/examples/recipes/ukb_ppp_pqtl/harmonise.sh
skills/locuscompare-region-render/licenses/clawbio/CITATION.cff
skills/locuscompare-region-render/licenses/clawbio/LICENSE
skills/locuscompare-region-render/tests/__init__.py
skills/locuscompare-region-render/tests/test_cli.py
skills/locuscompare-region-render/tests/test_gencode_ondemand.py
skills/locuscompare-region-render/tests/test_generate_synthetic_fixtures.py
skills/locuscompare-region-render/tests/test_golden_parity_sort1_dual_modality.py
skills/locuscompare-region-render/tests/test_live_locuscompare_region_render.py
skills/locuscompare-region-render/tests/test_locuscompare_region_render.py
skills/locuscompare-region-render/tests/test_prefetched.py
skills/locuscompare-region-render/tests/test_regional_plot.py
skills/locuscompare-region-render/tests/test_wald_ratio_types.py
skills/locuscompare-region-render/tests/fixtures/golden/sort1_dual_modality_eqtl_pqtl_ldl/expected.yaml
skills/locuscompare-region-render/tests/fixtures/golden/sort1_dual_modality_eqtl_pqtl_ldl/metadata.yaml
skills/locuscompare-region-render/tests/fixtures/golden/sort1_dual_modality_eqtl_pqtl_ldl/notes.md
skills/locuscompare-region-render/tests/fixtures/golden/sort1_dual_modality_eqtl_pqtl_ldl/inputs/eqtl_exposure_QTD000276_chr1_109_274_968_window.json.gz
skills/locuscompare-region-render/tests/fixtures/golden/sort1_dual_modality_eqtl_pqtl_ldl/inputs/gwas_outcome_GCST90269602_chr1_109_274_968_window.json.gz
skills/locuscompare-region-render/tests/fixtures/golden/sort1_dual_modality_eqtl_pqtl_ldl/inputs/pqtl_exposure_SORT1_EUR.json.gz
skills/locuszoom/DNAKIT.md
skills/locuszoom/LICENSE
skills/locuszoom/SKILL.md
skills/locuszoom/UPSTREAM.md
skills/locuszoom/references/LOCUSZOOMR.md
skills/locuszoom/references/upstream-readme.md
skills/locuszoom/scripts/locuszoom.py
skills/locuszoom/scripts/locuszoom_run.R
skills/long-read-sequencing-basecalling/DNAKIT.md
skills/long-read-sequencing-basecalling/SKILL.md
skills/long-read-sequencing-basecalling/UPSTREAM.md
skills/long-read-sequencing-basecalling/usage-guide.md
skills/long-read-sequencing-basecalling/examples/basecall_pipeline.sh
skills/long-read-sequencing-basecalling/examples/dorado_basecall.sh
skills/long-read-sequencing-basecalling/licenses/bioskills/LICENSE
skills/long-read-sequencing-clair3-variants/DNAKIT.md
skills/long-read-sequencing-clair3-variants/SKILL.md
skills/long-read-sequencing-clair3-variants/UPSTREAM.md
skills/long-read-sequencing-clair3-variants/usage-guide.md
skills/long-read-sequencing-clair3-variants/examples/clair3_workflow.sh
skills/long-read-sequencing-clair3-variants/licenses/bioskills/LICENSE
skills/long-read-sequencing-haplotype-phasing/DNAKIT.md
skills/long-read-sequencing-haplotype-phasing/SKILL.md
skills/long-read-sequencing-haplotype-phasing/UPSTREAM.md
skills/long-read-sequencing-haplotype-phasing/usage-guide.md
skills/long-read-sequencing-haplotype-phasing/examples/longphase_sv_cophasing.sh
skills/long-read-sequencing-haplotype-phasing/examples/phase_and_haplotag.sh
skills/long-read-sequencing-haplotype-phasing/licenses/bioskills/LICENSE
skills/long-read-sequencing-long-read-alignment/DNAKIT.md
skills/long-read-sequencing-long-read-alignment/SKILL.md
skills/long-read-sequencing-long-read-alignment/UPSTREAM.md
skills/long-read-sequencing-long-read-alignment/usage-guide.md
skills/long-read-sequencing-long-read-alignment/examples/methylation_passthrough.sh
skills/long-read-sequencing-long-read-alignment/examples/minimap2_align.sh
skills/long-read-sequencing-long-read-alignment/licenses/bioskills/LICENSE
skills/long-read-sequencing-long-read-qc/DNAKIT.md
skills/long-read-sequencing-long-read-qc/SKILL.md
skills/long-read-sequencing-long-read-qc/UPSTREAM.md
skills/long-read-sequencing-long-read-qc/usage-guide.md
skills/long-read-sequencing-long-read-qc/examples/qc_workflow.sh
skills/long-read-sequencing-long-read-qc/licenses/bioskills/LICENSE
skills/long-read-sequencing-medaka-polishing/DNAKIT.md
skills/long-read-sequencing-medaka-polishing/SKILL.md
skills/long-read-sequencing-medaka-polishing/UPSTREAM.md
skills/long-read-sequencing-medaka-polishing/usage-guide.md
skills/long-read-sequencing-medaka-polishing/examples/medaka_polish.sh
skills/long-read-sequencing-medaka-polishing/examples/medaka_variant.sh
skills/long-read-sequencing-medaka-polishing/licenses/bioskills/LICENSE
skills/long-read-sequencing-nanopore-methylation/DNAKIT.md
skills/long-read-sequencing-nanopore-methylation/SKILL.md
skills/long-read-sequencing-nanopore-methylation/UPSTREAM.md
skills/long-read-sequencing-nanopore-methylation/usage-guide.md
skills/long-read-sequencing-nanopore-methylation/examples/modkit_methylation.sh
skills/long-read-sequencing-nanopore-methylation/licenses/bioskills/LICENSE
skills/long-read-sequencing-structural-variants/DNAKIT.md
skills/long-read-sequencing-structural-variants/SKILL.md
skills/long-read-sequencing-structural-variants/UPSTREAM.md
skills/long-read-sequencing-structural-variants/usage-guide.md
skills/long-read-sequencing-structural-variants/examples/sv_calling.sh
skills/long-read-sequencing-structural-variants/licenses/bioskills/LICENSE
skills/longitudinal-monitoring/DNAKIT.md
skills/longitudinal-monitoring/SKILL.md
skills/longitudinal-monitoring/UPSTREAM.md
skills/longitudinal-monitoring/usage-guide.md
skills/longitudinal-monitoring/examples/longitudinal_monitoring.py
skills/longitudinal-monitoring/licenses/bioskills/LICENSE
skills/lorbin/DNAKIT.md
skills/lorbin/SKILL.md
skills/lorbin/UPSTREAM.md
skills/lorbin/licenses/pku-metagenomics/LICENSE
skills/lorbin/references/upstream-docs/compute-setup.md
skills/lorbin/references/upstream-docs/getting-started.md
skills/lorbin/references/upstream-docs/multi-platform.md
skills/lorbin/references/upstream-docs/public-databases.md
skills/lorbin/references/upstream-docs/references.md
skills/lorbin/references/upstream-docs/skills.md
skills/lorbin/references/upstream-docs/standard-pipeline.md
skills/lorbin/references/upstream-docs/tool-selection.md
skills/lorbin/references/upstream-docs/troubleshooting.md
skills/manhattan-qq/DNAKIT.md
skills/manhattan-qq/LICENSE
skills/manhattan-qq/SKILL.md
skills/manhattan-qq/UPSTREAM.md
skills/manhattan-qq/references/upstream-readme.md
skills/manhattan-qq/scripts/manhattan_qq.py
skills/mebs/DNAKIT.md
skills/mebs/SKILL.md
skills/mebs/UPSTREAM.md
skills/mebs/licenses/pku-metagenomics/LICENSE
skills/mebs/references/upstream-docs/compute-setup.md
skills/mebs/references/upstream-docs/getting-started.md
skills/mebs/references/upstream-docs/multi-platform.md
skills/mebs/references/upstream-docs/public-databases.md
skills/mebs/references/upstream-docs/references.md
skills/mebs/references/upstream-docs/skills.md
skills/mebs/references/upstream-docs/standard-pipeline.md
skills/mebs/references/upstream-docs/tool-selection.md
skills/mebs/references/upstream-docs/troubleshooting.md
skills/metabat2/DNAKIT.md
skills/metabat2/SKILL.md
skills/metabat2/UPSTREAM.md
skills/metabat2/agents/openai.yaml
skills/metabat2/licenses/pku-metagenomics/LICENSE
skills/metabat2/references/upstream-docs/compute-setup.md
skills/metabat2/references/upstream-docs/getting-started.md
skills/metabat2/references/upstream-docs/multi-platform.md
skills/metabat2/references/upstream-docs/public-databases.md
skills/metabat2/references/upstream-docs/references.md
skills/metabat2/references/upstream-docs/skills.md
skills/metabat2/references/upstream-docs/standard-pipeline.md
skills/metabat2/references/upstream-docs/tool-selection.md
skills/metabat2/references/upstream-docs/troubleshooting.md
skills/metabolic/DNAKIT.md
skills/metabolic/SKILL.md
skills/metabolic/UPSTREAM.md
skills/metabolic/licenses/pku-metagenomics/LICENSE
skills/metabolic/references/upstream-docs/compute-setup.md
skills/metabolic/references/upstream-docs/getting-started.md
skills/metabolic/references/upstream-docs/multi-platform.md
skills/metabolic/references/upstream-docs/public-databases.md
skills/metabolic/references/upstream-docs/references.md
skills/metabolic/references/upstream-docs/skills.md
skills/metabolic/references/upstream-docs/standard-pipeline.md
skills/metabolic/references/upstream-docs/tool-selection.md
skills/metabolic/references/upstream-docs/troubleshooting.md
skills/metagenomics-abundance/DNAKIT.md
skills/metagenomics-abundance/SKILL.md
skills/metagenomics-abundance/UPSTREAM.md
skills/metagenomics-abundance/usage-guide.md
skills/metagenomics-abundance/examples/bracken_abundance.sh
skills/metagenomics-abundance/examples/compositional_transform.py
skills/metagenomics-abundance/licenses/bioskills/LICENSE
skills/metagenomics-amr-detection/DNAKIT.md
skills/metagenomics-amr-detection/SKILL.md
skills/metagenomics-amr-detection/UPSTREAM.md
skills/metagenomics-amr-detection/usage-guide.md
skills/metagenomics-amr-detection/examples/batch_amr_screening.py
skills/metagenomics-amr-detection/examples/run_amrfinder.sh
skills/metagenomics-amr-detection/licenses/bioskills/LICENSE
skills/metagenomics-contamination-controls/DNAKIT.md
skills/metagenomics-contamination-controls/SKILL.md
skills/metagenomics-contamination-controls/UPSTREAM.md
skills/metagenomics-contamination-controls/usage-guide.md
skills/metagenomics-contamination-controls/examples/decontam_contaminants.R
skills/metagenomics-contamination-controls/examples/flag_kitome.py
skills/metagenomics-contamination-controls/examples/host_depletion.sh
skills/metagenomics-contamination-controls/licenses/bioskills/LICENSE
skills/metagenomics-functional-profiling/DNAKIT.md
skills/metagenomics-functional-profiling/SKILL.md
skills/metagenomics-functional-profiling/UPSTREAM.md
skills/metagenomics-functional-profiling/usage-guide.md
skills/metagenomics-functional-profiling/examples/humann_workflow.sh
skills/metagenomics-functional-profiling/licenses/bioskills/LICENSE
skills/metagenomics-kraken/DNAKIT.md
skills/metagenomics-kraken/SKILL.md
skills/metagenomics-kraken/UPSTREAM.md
skills/metagenomics-kraken/usage-guide.md
skills/metagenomics-kraken/examples/kraken2_classify.sh
skills/metagenomics-kraken/licenses/bioskills/LICENSE
skills/metagenomics-metaphlan/DNAKIT.md
skills/metagenomics-metaphlan/SKILL.md
skills/metagenomics-metaphlan/UPSTREAM.md
skills/metagenomics-metaphlan/usage-guide.md
skills/metagenomics-metaphlan/examples/metaphlan_profile.sh
skills/metagenomics-metaphlan/licenses/bioskills/LICENSE
skills/metagenomics-strain-tracking/DNAKIT.md
skills/metagenomics-strain-tracking/SKILL.md
skills/metagenomics-strain-tracking/UPSTREAM.md
skills/metagenomics-strain-tracking/usage-guide.md
skills/metagenomics-strain-tracking/examples/instrain_workflow.sh
skills/metagenomics-strain-tracking/examples/mash_comparison.sh
skills/metagenomics-strain-tracking/examples/parse_instrain_compare.py
skills/metagenomics-strain-tracking/licenses/bioskills/LICENSE
skills/metagenomics-visualization/DNAKIT.md
skills/metagenomics-visualization/SKILL.md
skills/metagenomics-visualization/UPSTREAM.md
skills/metagenomics-visualization/usage-guide.md
skills/metagenomics-visualization/examples/visualization_phyloseq.R
skills/metagenomics-visualization/examples/visualization_python.py
skills/metagenomics-visualization/licenses/bioskills/LICENSE
skills/methylation-aggregation/DNAKIT.md
skills/methylation-aggregation/SKILL.md
skills/methylation-aggregation/UPSTREAM.md
skills/methylation-aggregation/licenses/encode-toolkit/CITATION.cff
skills/methylation-aggregation/licenses/encode-toolkit/LICENSE
skills/methylation-aggregation/references/hmr-definitions.md
skills/methylation-aggregation/references/literature.md
skills/methylation-aggregation/scripts/validate_methylation.py
skills/methylation-array-preprocessing/DNAKIT.md
skills/methylation-array-preprocessing/SKILL.md
skills/methylation-array-preprocessing/UPSTREAM.md
skills/methylation-array-preprocessing/usage-guide.md
skills/methylation-array-preprocessing/examples/array_preprocessing.R
skills/methylation-array-preprocessing/licenses/bioskills/LICENSE
skills/methylation-array-qc-filtering/DNAKIT.md
skills/methylation-array-qc-filtering/SKILL.md
skills/methylation-array-qc-filtering/UPSTREAM.md
skills/methylation-array-qc-filtering/usage-guide.md
skills/methylation-array-qc-filtering/examples/array_qc_filtering.R
skills/methylation-array-qc-filtering/licenses/bioskills/LICENSE
skills/methylation-based-detection/DNAKIT.md
skills/methylation-based-detection/SKILL.md
skills/methylation-based-detection/UPSTREAM.md
skills/methylation-based-detection/usage-guide.md
skills/methylation-based-detection/examples/cfdna_methylation.py
skills/methylation-based-detection/licenses/bioskills/LICENSE
skills/methylation-bismark-alignment/DNAKIT.md
skills/methylation-bismark-alignment/SKILL.md
skills/methylation-bismark-alignment/UPSTREAM.md
skills/methylation-bismark-alignment/usage-guide.md
skills/methylation-bismark-alignment/examples/bismark_basic.sh
skills/methylation-bismark-alignment/licenses/bioskills/LICENSE
skills/methylation-calling/DNAKIT.md
skills/methylation-calling/SKILL.md
skills/methylation-calling/UPSTREAM.md
skills/methylation-calling/usage-guide.md
skills/methylation-calling/examples/extract_methylation.sh
skills/methylation-calling/licenses/bioskills/LICENSE
skills/methylation-cell-type-deconvolution/DNAKIT.md
skills/methylation-cell-type-deconvolution/SKILL.md
skills/methylation-cell-type-deconvolution/UPSTREAM.md
skills/methylation-cell-type-deconvolution/usage-guide.md
skills/methylation-cell-type-deconvolution/examples/cell_deconvolution.R
skills/methylation-cell-type-deconvolution/licenses/bioskills/LICENSE
skills/methylation-differential-cpg/DNAKIT.md
skills/methylation-differential-cpg/SKILL.md
skills/methylation-differential-cpg/UPSTREAM.md
skills/methylation-differential-cpg/usage-guide.md
skills/methylation-differential-cpg/examples/differential_methylation.py
skills/methylation-differential-cpg/examples/differential_methylation_limma.R
skills/methylation-differential-cpg/licenses/bioskills/LICENSE
skills/methylation-dmr-detection/DNAKIT.md
skills/methylation-dmr-detection/SKILL.md
skills/methylation-dmr-detection/UPSTREAM.md
skills/methylation-dmr-detection/usage-guide.md
skills/methylation-dmr-detection/examples/dmr_dmrseq.R
skills/methylation-dmr-detection/examples/dmr_methylkit.R
skills/methylation-dmr-detection/licenses/bioskills/LICENSE
skills/methylation-epigenetic-clocks/DNAKIT.md
skills/methylation-epigenetic-clocks/SKILL.md
skills/methylation-epigenetic-clocks/UPSTREAM.md
skills/methylation-epigenetic-clocks/usage-guide.md
skills/methylation-epigenetic-clocks/examples/epigenetic_clocks.R
skills/methylation-epigenetic-clocks/licenses/bioskills/LICENSE
skills/methylation-ewas-design/DNAKIT.md
skills/methylation-ewas-design/SKILL.md
skills/methylation-ewas-design/UPSTREAM.md
skills/methylation-ewas-design/usage-guide.md
skills/methylation-ewas-design/examples/ewas_sva_bacon.R
skills/methylation-ewas-design/examples/randomize_chip_layout.py
skills/methylation-ewas-design/licenses/bioskills/LICENSE
skills/methylation-methylkit/DNAKIT.md
skills/methylation-methylkit/SKILL.md
skills/methylation-methylkit/UPSTREAM.md
skills/methylation-methylkit/usage-guide.md
skills/methylation-methylkit/examples/methylkit_analysis.R
skills/methylation-methylkit/licenses/bioskills/LICENSE
skills/mgnify/DNAKIT.md
skills/mgnify/SKILL.md
skills/mgnify/UPSTREAM.md
skills/mgnify/agents/openai.yaml
skills/mgnify/licenses/pku-metagenomics/LICENSE
skills/mgnify/references/upstream-docs/compute-setup.md
skills/mgnify/references/upstream-docs/getting-started.md
skills/mgnify/references/upstream-docs/multi-platform.md
skills/mgnify/references/upstream-docs/public-databases.md
skills/mgnify/references/upstream-docs/references.md
skills/mgnify/references/upstream-docs/skills.md
skills/mgnify/references/upstream-docs/standard-pipeline.md
skills/mgnify/references/upstream-docs/tool-selection.md
skills/mgnify/references/upstream-docs/troubleshooting.md
skills/microbial-genome-characterization/DNAKIT.md
skills/microbial-genome-characterization/SKILL.md
skills/microbial-genome-characterization/UPSTREAM.md
skills/microbial-genome-characterization/evals/evals.json
skills/microbial-genome-characterization/licenses/tooluniverse/LICENSE
skills/microbial-mining/DNAKIT.md
skills/microbial-mining/SKILL.md
skills/microbial-mining/UPSTREAM.md
skills/microbial-mining/agents/openai.yaml
skills/microbial-mining/licenses/pku-metagenomics/LICENSE
skills/microbial-mining/references/upstream-docs/compute-setup.md
skills/microbial-mining/references/upstream-docs/getting-started.md
skills/microbial-mining/references/upstream-docs/multi-platform.md
skills/microbial-mining/references/upstream-docs/public-databases.md
skills/microbial-mining/references/upstream-docs/references.md
skills/microbial-mining/references/upstream-docs/skills.md
skills/microbial-mining/references/upstream-docs/standard-pipeline.md
skills/microbial-mining/references/upstream-docs/tool-selection.md
skills/microbial-mining/references/upstream-docs/troubleshooting.md
skills/microbiome-amplicon-processing/DNAKIT.md
skills/microbiome-amplicon-processing/SKILL.md
skills/microbiome-amplicon-processing/UPSTREAM.md
skills/microbiome-amplicon-processing/usage-guide.md
skills/microbiome-amplicon-processing/examples/dada2_workflow.R
skills/microbiome-amplicon-processing/examples/remove_primers.sh
skills/microbiome-amplicon-processing/licenses/bioskills/LICENSE
skills/microbiome-differential-abundance/DNAKIT.md
skills/microbiome-differential-abundance/SKILL.md
skills/microbiome-differential-abundance/UPSTREAM.md
skills/microbiome-differential-abundance/usage-guide.md
skills/microbiome-differential-abundance/examples/aldex2_analysis.R
skills/microbiome-differential-abundance/licenses/bioskills/LICENSE
skills/microbiome-diversity-analysis/DNAKIT.md
skills/microbiome-diversity-analysis/SKILL.md
skills/microbiome-diversity-analysis/UPSTREAM.md
skills/microbiome-diversity-analysis/usage-guide.md
skills/microbiome-diversity-analysis/examples/core_metrics_qiime2.sh
skills/microbiome-diversity-analysis/examples/diversity_analysis.R
skills/microbiome-diversity-analysis/licenses/bioskills/LICENSE
skills/microbiome-functional-prediction/DNAKIT.md
skills/microbiome-functional-prediction/SKILL.md
skills/microbiome-functional-prediction/UPSTREAM.md
skills/microbiome-functional-prediction/usage-guide.md
skills/microbiome-functional-prediction/examples/run_picrust2.sh
skills/microbiome-functional-prediction/licenses/bioskills/LICENSE
skills/microbiome-qiime2-workflow/DNAKIT.md
skills/microbiome-qiime2-workflow/SKILL.md
skills/microbiome-qiime2-workflow/UPSTREAM.md
skills/microbiome-qiime2-workflow/usage-guide.md
skills/microbiome-qiime2-workflow/examples/qiime2_16s.sh
skills/microbiome-qiime2-workflow/licenses/bioskills/LICENSE
skills/microbiome-research/DNAKIT.md
skills/microbiome-research/SKILL.md
skills/microbiome-research/UPSTREAM.md
skills/microbiome-research/licenses/tooluniverse/LICENSE
skills/microbiome-taxonomy-assignment/DNAKIT.md
skills/microbiome-taxonomy-assignment/SKILL.md
skills/microbiome-taxonomy-assignment/UPSTREAM.md
skills/microbiome-taxonomy-assignment/usage-guide.md
skills/microbiome-taxonomy-assignment/examples/assign_qiime2_region.sh
skills/microbiome-taxonomy-assignment/examples/assign_silva.R
skills/microbiome-taxonomy-assignment/licenses/bioskills/LICENSE
skills/mob-suite/DNAKIT.md
skills/mob-suite/SKILL.md
skills/mob-suite/UPSTREAM.md
skills/mob-suite/licenses/pku-metagenomics/LICENSE
skills/mob-suite/references/upstream-docs/compute-setup.md
skills/mob-suite/references/upstream-docs/getting-started.md
skills/mob-suite/references/upstream-docs/multi-platform.md
skills/mob-suite/references/upstream-docs/public-databases.md
skills/mob-suite/references/upstream-docs/references.md
skills/mob-suite/references/upstream-docs/skills.md
skills/mob-suite/references/upstream-docs/standard-pipeline.md
skills/mob-suite/references/upstream-docs/tool-selection.md
skills/mob-suite/references/upstream-docs/troubleshooting.md
skills/mobileelementfinder/DNAKIT.md
skills/mobileelementfinder/SKILL.md
skills/mobileelementfinder/UPSTREAM.md
skills/mobileelementfinder/licenses/pku-metagenomics/LICENSE
skills/mobileelementfinder/references/upstream-docs/compute-setup.md
skills/mobileelementfinder/references/upstream-docs/getting-started.md
skills/mobileelementfinder/references/upstream-docs/multi-platform.md
skills/mobileelementfinder/references/upstream-docs/public-databases.md
skills/mobileelementfinder/references/upstream-docs/references.md
skills/mobileelementfinder/references/upstream-docs/skills.md
skills/mobileelementfinder/references/upstream-docs/standard-pipeline.md
skills/mobileelementfinder/references/upstream-docs/tool-selection.md
skills/mobileelementfinder/references/upstream-docs/troubleshooting.md
skills/mobileog/DNAKIT.md
skills/mobileog/SKILL.md
skills/mobileog/UPSTREAM.md
skills/mobileog/licenses/pku-metagenomics/LICENSE
skills/mobileog/references/upstream-docs/compute-setup.md
skills/mobileog/references/upstream-docs/getting-started.md
skills/mobileog/references/upstream-docs/multi-platform.md
skills/mobileog/references/upstream-docs/public-databases.md
skills/mobileog/references/upstream-docs/references.md
skills/mobileog/references/upstream-docs/skills.md
skills/mobileog/references/upstream-docs/standard-pipeline.md
skills/mobileog/references/upstream-docs/tool-selection.md
skills/mobileog/references/upstream-docs/troubleshooting.md
skills/model-organism-genetics/DNAKIT.md
skills/model-organism-genetics/SKILL.md
skills/model-organism-genetics/UPSTREAM.md
skills/model-organism-genetics/licenses/tooluniverse/LICENSE
skills/molecular-cloning/DNAKIT.md
skills/molecular-cloning/SKILL.md
skills/molecular-cloning/UPSTREAM.md
skills/molecular-cloning/test_cloning_qc.py
skills/molecular-cloning/licenses/tooluniverse/LICENSE
skills/molecular-cloning/scripts/cloning_qc.py
skills/monarch-database/DNAKIT.md
skills/monarch-database/SKILL.md
skills/monarch-database/UPSTREAM.md
skills/monarch-database/licenses/kdense/CITATION.cff
skills/monarch-database/licenses/kdense/LICENSE.md
skills/monarch-database/licenses/sciagent/CC-BY-4.0.txt
skills/monarch-database/licenses/sciagent/LICENSE
skills/monarch-database/licenses/tooluniverse/LICENSE
skills/motif-search/DNAKIT.md
skills/motif-search/SKILL.md
skills/motif-search/UPSTREAM.md
skills/motif-search/usage-guide.md
skills/motif-search/examples/basic_search.py
skills/motif-search/examples/motif_files.py
skills/motif-search/examples/pwm_search.py
skills/motif-search/examples/regex_search.py
skills/motif-search/licenses/bioskills/LICENSE
skills/mouse-phenome-database/DNAKIT.md
skills/mouse-phenome-database/SKILL.md
skills/mouse-phenome-database/UPSTREAM.md
skills/mouse-phenome-database/licenses/kdense/CITATION.cff
skills/mouse-phenome-database/licenses/kdense/LICENSE.md
skills/mouse-phenome-database/licenses/sciagent/CC-BY-4.0.txt
skills/mouse-phenome-database/licenses/sciagent/LICENSE
skills/mouse-phenome-database/licenses/tooluniverse/LICENSE
skills/multi-omics-data-harmonization/DNAKIT.md
skills/multi-omics-data-harmonization/SKILL.md
skills/multi-omics-data-harmonization/UPSTREAM.md
skills/multi-omics-data-harmonization/usage-guide.md
skills/multi-omics-data-harmonization/examples/harmonize_data.R
skills/multi-omics-data-harmonization/licenses/bioskills/LICENSE
skills/multi-omics-integration/DNAKIT.md
skills/multi-omics-integration/SKILL.md
skills/multi-omics-integration/UPSTREAM.md
skills/multi-omics-integration/phase_details.md
skills/multi-omics-integration/licenses/tooluniverse/LICENSE
skills/multi-omics-mixomics-analysis/DNAKIT.md
skills/multi-omics-mixomics-analysis/SKILL.md
skills/multi-omics-mixomics-analysis/UPSTREAM.md
skills/multi-omics-mixomics-analysis/usage-guide.md
skills/multi-omics-mixomics-analysis/examples/diablo_workflow.R
skills/multi-omics-mixomics-analysis/licenses/bioskills/LICENSE
skills/multi-omics-mofa-integration/DNAKIT.md
skills/multi-omics-mofa-integration/SKILL.md
skills/multi-omics-mofa-integration/UPSTREAM.md
skills/multi-omics-mofa-integration/usage-guide.md
skills/multi-omics-mofa-integration/examples/mofa_workflow.R
skills/multi-omics-mofa-integration/licenses/bioskills/LICENSE
skills/multiomic-disease-characterization/.env.template
skills/multiomic-disease-characterization/DNAKIT.md
skills/multiomic-disease-characterization/SKILL.md
skills/multiomic-disease-characterization/UPSTREAM.md
skills/multiomic-disease-characterization/integration-scoring.md
skills/multiomic-disease-characterization/report-template.md
skills/multiomic-disease-characterization/response-formats.md
skills/multiomic-disease-characterization/test_multiomic_disease.py
skills/multiomic-disease-characterization/tool-reference.md
skills/multiomic-disease-characterization/use-patterns.md
skills/multiomic-disease-characterization/licenses/tooluniverse/LICENSE
skills/multiqc-reporter/DNAKIT.md
skills/multiqc-reporter/SKILL.md
skills/multiqc-reporter/UPSTREAM.md
skills/multiqc-reporter/multiqc_reporter.py
skills/multiqc-reporter/licenses/clawbio/CITATION.cff
skills/multiqc-reporter/licenses/clawbio/LICENSE
skills/multiqc-reporter/tests/__init__.py
skills/multiqc-reporter/tests/test_multiqc_reporter.py
skills/ncbi-datasets-cli/DNAKIT.md
skills/ncbi-datasets-cli/SKILL.md
skills/ncbi-datasets-cli/UPSTREAM.md
skills/ncbi-datasets-cli/usage-guide.md
skills/ncbi-datasets-cli/examples/bulk_dehydrated.sh
skills/ncbi-datasets-cli/examples/download_genome.sh
skills/ncbi-datasets-cli/examples/gene_metadata.sh
skills/ncbi-datasets-cli/licenses/bioskills/LICENSE
skills/nextflow-development/DNAKIT.md
skills/nextflow-development/LICENSE
skills/nextflow-development/LICENSE.txt
skills/nextflow-development/SKILL.md
skills/nextflow-development/UPSTREAM.md
skills/nextflow-development/references/geo-sra-acquisition.md
skills/nextflow-development/references/installation.md
skills/nextflow-development/references/troubleshooting.md
skills/nextflow-development/references/upstream-readme.md
skills/nextflow-development/references/pipelines/atacseq.md
skills/nextflow-development/references/pipelines/rnaseq.md
skills/nextflow-development/references/pipelines/sarek.md
skills/nextflow-development/scripts/check_environment.py
skills/nextflow-development/scripts/detect_data_type.py
skills/nextflow-development/scripts/generate_samplesheet.py
skills/nextflow-development/scripts/manage_genomes.py
skills/nextflow-development/scripts/sra_geo_fetch.py
skills/nextflow-development/scripts/config/genomes.yaml
skills/nextflow-development/scripts/config/pipelines/atacseq.yaml
skills/nextflow-development/scripts/config/pipelines/rnaseq.yaml
skills/nextflow-development/scripts/config/pipelines/sarek.yaml
skills/nextflow-development/scripts/utils/__init__.py
skills/nextflow-development/scripts/utils/file_discovery.py
skills/nextflow-development/scripts/utils/ncbi_utils.py
skills/nextflow-development/scripts/utils/sample_inference.py
skills/nextflow-development/scripts/utils/validators.py
skills/nfcore-sarek-wrapper/.gitignore
skills/nfcore-sarek-wrapper/CHANGELOG.md
skills/nfcore-sarek-wrapper/DNAKIT.md
skills/nfcore-sarek-wrapper/README.md
skills/nfcore-sarek-wrapper/SKILL.md
skills/nfcore-sarek-wrapper/UPSTREAM.md
skills/nfcore-sarek-wrapper/_isolated_imports.py
skills/nfcore-sarek-wrapper/command_builder.py
skills/nfcore-sarek-wrapper/errors.py
skills/nfcore-sarek-wrapper/executor.py
skills/nfcore-sarek-wrapper/nfcore_sarek_wrapper.py
skills/nfcore-sarek-wrapper/outputs_parser.py
skills/nfcore-sarek-wrapper/params_builder.py
skills/nfcore-sarek-wrapper/pipeline_source.py
skills/nfcore-sarek-wrapper/preflight.py
skills/nfcore-sarek-wrapper/provenance.py
skills/nfcore-sarek-wrapper/remap_paths.py
skills/nfcore-sarek-wrapper/reporting.py
skills/nfcore-sarek-wrapper/samplesheet_builder.py
skills/nfcore-sarek-wrapper/schemas.py
skills/nfcore-sarek-wrapper/demo/README.md
skills/nfcore-sarek-wrapper/licenses/clawbio/CITATION.cff
skills/nfcore-sarek-wrapper/licenses/clawbio/LICENSE
skills/nfcore-sarek-wrapper/reproducibility/compatibility_policy.json
skills/nfcore-sarek-wrapper/reproducibility/pinned_versions.json
skills/nfcore-sarek-wrapper/tests/conftest.py
skills/nfcore-sarek-wrapper/tests/preflight_fixtures.py
skills/nfcore-sarek-wrapper/tests/test_catalog_consistency.py
skills/nfcore-sarek-wrapper/tests/test_cli_direct_invocation.py
skills/nfcore-sarek-wrapper/tests/test_current_audit_regressions.py
skills/nfcore-sarek-wrapper/tests/test_executor.py
skills/nfcore-sarek-wrapper/tests/test_nfcore_sarek_wrapper.py
skills/nfcore-sarek-wrapper/tests/test_outputs_parser.py
skills/nfcore-sarek-wrapper/tests/test_params_builder.py
skills/nfcore-sarek-wrapper/tests/test_portability_remap_interpreter.py
skills/nfcore-sarek-wrapper/tests/test_preflight.py
skills/nfcore-sarek-wrapper/tests/test_provenance.py
skills/nfcore-sarek-wrapper/tests/test_remap_paths.py
skills/nfcore-sarek-wrapper/tests/test_reporting.py
skills/nfcore-sarek-wrapper/tests/test_samplesheet_builder.py
skills/ngs-tertiary-analysis/DNAKIT.md
skills/ngs-tertiary-analysis/SKILL.md
skills/ngs-tertiary-analysis/UPSTREAM.md
skills/ngs-tertiary-analysis/examples.md
skills/ngs-tertiary-analysis/reference.md
skills/ngs-tertiary-analysis/licenses/ngs-tertiary/LICENSE
skills/nucleotide-transformer/DNAKIT.md
skills/nucleotide-transformer/SKILL.md
skills/nucleotide-transformer/UPSTREAM.md
skills/nucleotide-transformer/licenses/pku-metagenomics/LICENSE
skills/nucleotide-transformer/references/upstream-docs/compute-setup.md
skills/nucleotide-transformer/references/upstream-docs/getting-started.md
skills/nucleotide-transformer/references/upstream-docs/multi-platform.md
skills/nucleotide-transformer/references/upstream-docs/public-databases.md
skills/nucleotide-transformer/references/upstream-docs/references.md
skills/nucleotide-transformer/references/upstream-docs/skills.md
skills/nucleotide-transformer/references/upstream-docs/standard-pipeline.md
skills/nucleotide-transformer/references/upstream-docs/tool-selection.md
skills/nucleotide-transformer/references/upstream-docs/troubleshooting.md
skills/okg-search/DNAKIT.md
skills/okg-search/LICENSE
skills/okg-search/SKILL.md
skills/okg-search/UPSTREAM.md
skills/okg-search/references/upstream-readme.md
skills/okg-search/scripts/okg_search.py
skills/omg/DNAKIT.md
skills/omg/SKILL.md
skills/omg/UPSTREAM.md
skills/omg/licenses/pku-metagenomics/LICENSE
skills/omg/references/upstream-docs/compute-setup.md
skills/omg/references/upstream-docs/getting-started.md
skills/omg/references/upstream-docs/multi-platform.md
skills/omg/references/upstream-docs/public-databases.md
skills/omg/references/upstream-docs/references.md
skills/omg/references/upstream-docs/skills.md
skills/omg/references/upstream-docs/standard-pipeline.md
skills/omg/references/upstream-docs/tool-selection.md
skills/omg/references/upstream-docs/troubleshooting.md
skills/onekgpd-individual-queries/DNAKIT.md
skills/onekgpd-individual-queries/LICENSE
skills/onekgpd-individual-queries/SKILL.md
skills/onekgpd-individual-queries/UPSTREAM.md
skills/onekgpd-individual-queries/assets/kgpe.json
skills/onekgpd-individual-queries/references/annotation_vocabularies.md
skills/onekgpd-individual-queries/references/onekgpd_commands.md
skills/onekgpd-individual-queries/references/upstream-readme.md
skills/onekgpd-individual-queries/scripts/onekgpd_api.py
skills/onekgpd-individual-queries/scripts/onekgpd_meta.py
skills/optimize-hifi-diploid-assembly/DNAKIT.md
skills/optimize-hifi-diploid-assembly/SKILL.md
skills/optimize-hifi-diploid-assembly/UPSTREAM.md
skills/optimize-hifi-diploid-assembly/licenses/myriad/CITATION.cff
skills/optimize-hifi-diploid-assembly/licenses/myriad/LICENSE-APACHE-2.0.txt
skills/optimize-hifi-diploid-assembly/licenses/myriad/LICENSE-CC-BY-4.0.txt
skills/optimize-hifi-diploid-assembly/licenses/myriad/LICENSE.md
skills/optimize-hifi-diploid-assembly/licenses/myriad/NOTICE.md
skills/ortholog-inference/DNAKIT.md
skills/ortholog-inference/SKILL.md
skills/ortholog-inference/UPSTREAM.md
skills/ortholog-inference/usage-guide.md
skills/ortholog-inference/examples/compara_orthologs.py
skills/ortholog-inference/examples/cross_resource.py
skills/ortholog-inference/examples/kegg_orthology.py
skills/ortholog-inference/licenses/bioskills/LICENSE
skills/outlier-splicing-detection/DNAKIT.md
skills/outlier-splicing-detection/LICENSE
skills/outlier-splicing-detection/SKILL.md
skills/outlier-splicing-detection/UPSTREAM.md
skills/outlier-splicing-detection/usage-guide.md
skills/outlier-splicing-detection/examples/fraser2_rare_disease.R
skills/outlier-splicing-detection/references/upstream-readme.md
skills/paired-end-fastq/DNAKIT.md
skills/paired-end-fastq/SKILL.md
skills/paired-end-fastq/UPSTREAM.md
skills/paired-end-fastq/usage-guide.md
skills/paired-end-fastq/examples/paired_end_io.py
skills/paired-end-fastq/licenses/bioskills/LICENSE
skills/parabricks/.skillsource.json
skills/parabricks/DNAKIT.md
skills/parabricks/SKILL.md
skills/parabricks/UPSTREAM.md
skills/parabricks/evals/evals.json
skills/parabricks/licenses/bionemo/LICENSE
skills/parabricks/licenses/bionemo/LICENSE-APACHE-2.0
skills/parabricks/licenses/bionemo/LICENSE-CC-BY-4.0
skills/parabricks/licenses/bionemo/NOTICE
skills/parabricks/references/parabricks-rna-validate.md
skills/parabricks/references/pbrun-applybqsr.md
skills/parabricks/references/pbrun-bam2fq.md
skills/parabricks/references/pbrun-bammetrics.md
skills/parabricks/references/pbrun-bamsort.md
skills/parabricks/references/pbrun-bqsr.md
skills/parabricks/references/pbrun-collectmultiplemetrics.md
skills/parabricks/references/pbrun-dbsnp.md
skills/parabricks/references/pbrun-deepsomatic.md
skills/parabricks/references/pbrun-deepvariant.md
skills/parabricks/references/pbrun-deepvariant_germline.md
skills/parabricks/references/pbrun-fq2bam.md
skills/parabricks/references/pbrun-fq2bam_meth.md
skills/parabricks/references/pbrun-genotypegvcf.md
skills/parabricks/references/pbrun-germline.md
skills/parabricks/references/pbrun-giraffe.md
skills/parabricks/references/pbrun-haplotypecaller.md
skills/parabricks/references/pbrun-indexgvcf.md
skills/parabricks/references/pbrun-markdup.md
skills/parabricks/references/pbrun-minimap2.md
skills/parabricks/references/pbrun-mutectcaller.md
skills/parabricks/references/pbrun-ont_germline.md
skills/parabricks/references/pbrun-pacbio_germline.md
skills/parabricks/references/pbrun-pangenome_aware_deepvariant.md
skills/parabricks/references/pbrun-pangenome_germline.md
skills/parabricks/references/pbrun-postpon.md
skills/parabricks/references/pbrun-prepon.md
skills/parabricks/references/pbrun-rna_fq2bam.md
skills/parabricks/references/pbrun-somatic.md
skills/parabricks/references/pbrun-starfusion.md
skills/parabricks/references/performance.md
skills/parabricks/references/runtime-environment.md
skills/parabricks/references/tool-index.md
skills/parabricks/scripts/check_parabricks_runtime.py
skills/pathogen-variant-surveillance/DNAKIT.md
skills/pathogen-variant-surveillance/SKILL.md
skills/pathogen-variant-surveillance/UPSTREAM.md
skills/pathogen-variant-surveillance/licenses/kdense/CITATION.cff
skills/pathogen-variant-surveillance/licenses/kdense/LICENSE.md
skills/pathogen-variant-surveillance/references/lapis-api.md
skills/pathogen-variant-surveillance/references/lineage-nomenclature.md
skills/pathogen-variant-surveillance/references/surveillance-caveats.md
skills/pathogen-variant-surveillance/scripts/lapis_client.py
skills/pathogen-variant-surveillance/scripts/lineage_prevalence.py
skills/pathogen-variant-surveillance/scripts/mutation_profile.py
skills/pathogen-variant-surveillance/scripts/reporting_lag.py
skills/pathogen-variant-surveillance/scripts/resolve_lineage.py
skills/pathway-disease-genetics/DNAKIT.md
skills/pathway-disease-genetics/SKILL.md
skills/pathway-disease-genetics/UPSTREAM.md
skills/pathway-disease-genetics/licenses/tooluniverse/LICENSE
skills/pdb-database/DNAKIT.md
skills/pdb-database/LICENSE
skills/pdb-database/SKILL.md
skills/pdb-database/SKILL_LICENSES.md
skills/pdb-database/UPSTREAM.md
skills/pdb-database/references/citation.bib
skills/pdb-database/references/upstream-readme.md
skills/pdb-database/references/uv/SKILL.md
skills/pdb-database/scripts/download_coordinate_files.py
skills/pdb-database/scripts/fetch_pdb_metadata.py
skills/pdb-database/scripts/fetch_schema.py
skills/pdb-database/scripts/search_pdb.py
skills/phasing-imputation-genotype-imputation/DNAKIT.md
skills/phasing-imputation-genotype-imputation/SKILL.md
skills/phasing-imputation-genotype-imputation/UPSTREAM.md
skills/phasing-imputation-genotype-imputation/usage-guide.md
skills/phasing-imputation-genotype-imputation/examples/run_beagle_imputation.sh
skills/phasing-imputation-genotype-imputation/licenses/bioskills/LICENSE
skills/phasing-imputation-haplotype-phasing/DNAKIT.md
skills/phasing-imputation-haplotype-phasing/SKILL.md
skills/phasing-imputation-haplotype-phasing/UPSTREAM.md
skills/phasing-imputation-haplotype-phasing/usage-guide.md
skills/phasing-imputation-haplotype-phasing/examples/run_shapeit.sh
skills/phasing-imputation-haplotype-phasing/licenses/bioskills/LICENSE
skills/phasing-imputation-imputation-qc/DNAKIT.md
skills/phasing-imputation-imputation-qc/SKILL.md
skills/phasing-imputation-imputation-qc/UPSTREAM.md
skills/phasing-imputation-imputation-qc/usage-guide.md
skills/phasing-imputation-imputation-qc/examples/imputation_qc.py
skills/phasing-imputation-imputation-qc/licenses/bioskills/LICENSE
skills/phasing-imputation-reference-panels/DNAKIT.md
skills/phasing-imputation-reference-panels/SKILL.md
skills/phasing-imputation-reference-panels/UPSTREAM.md
skills/phasing-imputation-reference-panels/usage-guide.md
skills/phasing-imputation-reference-panels/examples/prepare_panel.sh
skills/phasing-imputation-reference-panels/licenses/bioskills/LICENSE
skills/phewas/DNAKIT.md
skills/phewas/SKILL.md
skills/phewas/UPSTREAM.md
skills/phewas/evals/evals.json
skills/phewas/licenses/tooluniverse/LICENSE
skills/phylign/DNAKIT.md
skills/phylign/SKILL.md
skills/phylign/UPSTREAM.md
skills/phylign/licenses/pku-metagenomics/LICENSE
skills/phylign/references/upstream-docs/compute-setup.md
skills/phylign/references/upstream-docs/getting-started.md
skills/phylign/references/upstream-docs/multi-platform.md
skills/phylign/references/upstream-docs/public-databases.md
skills/phylign/references/upstream-docs/references.md
skills/phylign/references/upstream-docs/skills.md
skills/phylign/references/upstream-docs/standard-pipeline.md
skills/phylign/references/upstream-docs/tool-selection.md
skills/phylign/references/upstream-docs/troubleshooting.md
skills/phylo-bayesian-inference/DNAKIT.md
skills/phylo-bayesian-inference/SKILL.md
skills/phylo-bayesian-inference/UPSTREAM.md
skills/phylo-bayesian-inference/usage-guide.md
skills/phylo-bayesian-inference/examples/bayesian_convergence.py
skills/phylo-bayesian-inference/licenses/bioskills/LICENSE
skills/phylo-distance-calculations/DNAKIT.md
skills/phylo-distance-calculations/SKILL.md
skills/phylo-distance-calculations/UPSTREAM.md
skills/phylo-distance-calculations/usage-guide.md
skills/phylo-distance-calculations/examples/bootstrap_consensus.py
skills/phylo-distance-calculations/examples/build_nj_tree.py
skills/phylo-distance-calculations/examples/model_corrected_tree.R
skills/phylo-distance-calculations/examples/pairwise_tree_distances.py
skills/phylo-distance-calculations/licenses/bioskills/LICENSE
skills/phylo-divergence-dating/DNAKIT.md
skills/phylo-divergence-dating/SKILL.md
skills/phylo-divergence-dating/UPSTREAM.md
skills/phylo-divergence-dating/usage-guide.md
skills/phylo-divergence-dating/examples/mcmctree_setup.py
skills/phylo-divergence-dating/licenses/bioskills/LICENSE
skills/phylo-modern-tree-inference/DNAKIT.md
skills/phylo-modern-tree-inference/SKILL.md
skills/phylo-modern-tree-inference/UPSTREAM.md
skills/phylo-modern-tree-inference/usage-guide.md
skills/phylo-modern-tree-inference/examples/iqtree_basic.sh
skills/phylo-modern-tree-inference/examples/partitioned_analysis.sh
skills/phylo-modern-tree-inference/examples/raxml_analysis.sh
skills/phylo-modern-tree-inference/licenses/bioskills/LICENSE
skills/phylo-species-trees/DNAKIT.md
skills/phylo-species-trees/SKILL.md
skills/phylo-species-trees/UPSTREAM.md
skills/phylo-species-trees/usage-guide.md
skills/phylo-species-trees/examples/astral_pipeline.sh
skills/phylo-species-trees/licenses/bioskills/LICENSE
skills/phylo-tree-io/DNAKIT.md
skills/phylo-tree-io/SKILL.md
skills/phylo-tree-io/UPSTREAM.md
skills/phylo-tree-io/usage-guide.md
skills/phylo-tree-io/examples/convert_formats.py
skills/phylo-tree-io/examples/parse_multiple_trees.py
skills/phylo-tree-io/examples/read_newick.py
skills/phylo-tree-io/licenses/bioskills/LICENSE
skills/phylo-tree-manipulation/DNAKIT.md
skills/phylo-tree-manipulation/SKILL.md
skills/phylo-tree-manipulation/UPSTREAM.md
skills/phylo-tree-manipulation/usage-guide.md
skills/phylo-tree-manipulation/examples/collapse_support.py
skills/phylo-tree-manipulation/examples/common_ancestor.py
skills/phylo-tree-manipulation/examples/prune_taxa.py
skills/phylo-tree-manipulation/examples/root_tree.py
skills/phylo-tree-manipulation/licenses/bioskills/LICENSE
skills/phylo-tree-visualization/DNAKIT.md
skills/phylo-tree-visualization/SKILL.md
skills/phylo-tree-visualization/UPSTREAM.md
skills/phylo-tree-visualization/usage-guide.md
skills/phylo-tree-visualization/examples/ascii_tree.py
skills/phylo-tree-visualization/examples/basic_tree_plot.py
skills/phylo-tree-visualization/examples/labeled_tree.py
skills/phylo-tree-visualization/licenses/bioskills/LICENSE
skills/phylogenomics/DNAKIT.md
skills/phylogenomics/SKILL.md
skills/phylogenomics/UPSTREAM.md
skills/phylogenomics/docs/README.md
skills/phylogenomics/docs/ete-toolkit.md
skills/phylogenomics/docs/iqtree.md
skills/phylogenomics/docs/veryfasttree.md
skills/phylogenomics/fixtures/marker.faa
skills/phylogenomics/fixtures/markers.tsv
skills/phylogenomics/fixtures/reference.faa
skills/phylogenomics/fixtures/references.tsv
skills/phylogenomics/fixtures/tree.nwk
skills/phylogenomics/licenses/omics/LICENSE
skills/phylogenomics/scripts/run_phylogenomics.py
skills/pileup-generation/DNAKIT.md
skills/pileup-generation/SKILL.md
skills/pileup-generation/UPSTREAM.md
skills/pileup-generation/usage-guide.md
skills/pileup-generation/examples/allele_counts.py
skills/pileup-generation/licenses/bioskills/LICENSE
skills/pipeline-dnaseseq/DNAKIT.md
skills/pipeline-dnaseseq/SKILL.md
skills/pipeline-dnaseseq/UPSTREAM.md
skills/pipeline-dnaseseq/licenses/encode-toolkit/CITATION.cff
skills/pipeline-dnaseseq/licenses/encode-toolkit/LICENSE
skills/pipeline-dnaseseq/references/01-qc-trimming.md
skills/pipeline-dnaseseq/references/02-alignment.md
skills/pipeline-dnaseseq/references/03-filtering.md
skills/pipeline-dnaseseq/references/04-hotspot-calling.md
skills/pipeline-dnaseseq/references/05-footprinting.md
skills/pipeline-dnaseseq/references/literature.md
skills/pipeline-dnaseseq/scripts/Dockerfile
skills/pipeline-dnaseseq/scripts/main.nf
skills/pipeline-dnaseseq/scripts/nextflow.config
skills/pipeline-guide/DNAKIT.md
skills/pipeline-guide/SKILL.md
skills/pipeline-guide/UPSTREAM.md
skills/pipeline-guide/licenses/encode-toolkit/CITATION.cff
skills/pipeline-guide/licenses/encode-toolkit/LICENSE
skills/pipeline-guide/references/literature.md
skills/plannotate-plasmid-annotation/DNAKIT.md
skills/plannotate-plasmid-annotation/SKILL.md
skills/plannotate-plasmid-annotation/UPSTREAM.md
skills/plannotate-plasmid-annotation/licenses/kdense/CITATION.cff
skills/plannotate-plasmid-annotation/licenses/kdense/LICENSE.md
skills/plannotate-plasmid-annotation/licenses/sciagent/CC-BY-4.0.txt
skills/plannotate-plasmid-annotation/licenses/sciagent/LICENSE
skills/plannotate-plasmid-annotation/licenses/tooluniverse/LICENSE
skills/plant-genome-guided-primer-design/CITATION.cff
skills/plant-genome-guided-primer-design/DNAKIT.md
skills/plant-genome-guided-primer-design/LICENSE
skills/plant-genome-guided-primer-design/README.md
skills/plant-genome-guided-primer-design/SKILL.md
skills/plant-genome-guided-primer-design/UPSTREAM.md
skills/plant-genome-guided-primer-design/licenses/plant-qpcr/CITATION.cff
skills/plant-genome-guided-primer-design/licenses/plant-qpcr/LICENSE
skills/plant-genomics/DNAKIT.md
skills/plant-genomics/SKILL.md
skills/plant-genomics/UPSTREAM.md
skills/plant-genomics/licenses/tooluniverse/LICENSE
skills/plant-omics-db/DNAKIT.md
skills/plant-omics-db/SKILL.md
skills/plant-omics-db/UPSTREAM.md
skills/plant-omics-db/licenses/plant-skills/LICENSE
skills/plasmaag/DNAKIT.md
skills/plasmaag/SKILL.md
skills/plasmaag/UPSTREAM.md
skills/plasmaag/licenses/pku-metagenomics/LICENSE
skills/plasmaag/references/upstream-docs/compute-setup.md
skills/plasmaag/references/upstream-docs/getting-started.md
skills/plasmaag/references/upstream-docs/multi-platform.md
skills/plasmaag/references/upstream-docs/public-databases.md
skills/plasmaag/references/upstream-docs/references.md
skills/plasmaag/references/upstream-docs/skills.md
skills/plasmaag/references/upstream-docs/standard-pipeline.md
skills/plasmaag/references/upstream-docs/tool-selection.md
skills/plasmaag/references/upstream-docs/troubleshooting.md
skills/pod5/CHANGELOG.md
skills/pod5/DNAKIT.md
skills/pod5/SKILL.md
skills/pod5/UPSTREAM.md
skills/pod5/environment.yaml
skills/pod5/patterns.md
skills/pod5/reference.md
skills/pod5/licenses/damlab/LICENSE
skills/polyploid-gene-family-cloning/CITATION.cff
skills/polyploid-gene-family-cloning/DNAKIT.md
skills/polyploid-gene-family-cloning/LICENSE
skills/polyploid-gene-family-cloning/README.md
skills/polyploid-gene-family-cloning/SKILL.md
skills/polyploid-gene-family-cloning/UPSTREAM.md
skills/polyploid-gene-family-cloning/environment_consistency_check/check_env.py
skills/polyploid-gene-family-cloning/environment_consistency_check/operating_manual.txt
skills/polyploid-gene-family-cloning/licenses/polyploid-cloning/CITATION.cff
skills/polyploid-gene-family-cloning/licenses/polyploid-cloning/LICENSE
skills/population-genetics-1000genomes/DNAKIT.md
skills/population-genetics-1000genomes/SKILL.md
skills/population-genetics-1000genomes/UPSTREAM.md
skills/population-genetics-1000genomes/licenses/tooluniverse/LICENSE
skills/population-genetics-association-testing/DNAKIT.md
skills/population-genetics-association-testing/SKILL.md
skills/population-genetics-association-testing/UPSTREAM.md
skills/population-genetics-association-testing/usage-guide.md
skills/population-genetics-association-testing/examples/gwas_pipeline.sh
skills/population-genetics-association-testing/licenses/bioskills/LICENSE
skills/population-genetics-linkage-disequilibrium/DNAKIT.md
skills/population-genetics-linkage-disequilibrium/SKILL.md
skills/population-genetics-linkage-disequilibrium/UPSTREAM.md
skills/population-genetics-linkage-disequilibrium/usage-guide.md
skills/population-genetics-linkage-disequilibrium/examples/ld_analysis.sh
skills/population-genetics-linkage-disequilibrium/licenses/bioskills/LICENSE
skills/population-genetics-plink-basics/DNAKIT.md
skills/population-genetics-plink-basics/SKILL.md
skills/population-genetics-plink-basics/UPSTREAM.md
skills/population-genetics-plink-basics/usage-guide.md
skills/population-genetics-plink-basics/examples/qc_pipeline.sh
skills/population-genetics-plink-basics/licenses/bioskills/LICENSE
skills/population-genetics-population-structure/DNAKIT.md
skills/population-genetics-population-structure/SKILL.md
skills/population-genetics-population-structure/UPSTREAM.md
skills/population-genetics-population-structure/usage-guide.md
skills/population-genetics-population-structure/examples/structure_analysis.sh
skills/population-genetics-population-structure/licenses/bioskills/LICENSE
skills/population-genetics-rare-variant-association/DNAKIT.md
skills/population-genetics-rare-variant-association/SKILL.md
skills/population-genetics-rare-variant-association/UPSTREAM.md
skills/population-genetics-rare-variant-association/usage-guide.md
skills/population-genetics-rare-variant-association/examples/rare_variant_test.sh
skills/population-genetics-rare-variant-association/licenses/bioskills/LICENSE
skills/population-genetics-scikit-allel-analysis/DNAKIT.md
skills/population-genetics-scikit-allel-analysis/SKILL.md
skills/population-genetics-scikit-allel-analysis/UPSTREAM.md
skills/population-genetics-scikit-allel-analysis/usage-guide.md
skills/population-genetics-scikit-allel-analysis/examples/basic_analysis.py
skills/population-genetics-scikit-allel-analysis/licenses/bioskills/LICENSE
skills/population-genetics-selection-statistics/DNAKIT.md
skills/population-genetics-selection-statistics/SKILL.md
skills/population-genetics-selection-statistics/UPSTREAM.md
skills/population-genetics-selection-statistics/usage-guide.md
skills/population-genetics-selection-statistics/examples/selection_scan.py
skills/population-genetics-selection-statistics/licenses/bioskills/LICENSE
skills/prefect-dask-nextflow/DNAKIT.md
skills/prefect-dask-nextflow/SKILL.md
skills/prefect-dask-nextflow/UPSTREAM.md
skills/prefect-dask-nextflow/decision-matrix.md
skills/prefect-dask-nextflow/examples.md
skills/prefect-dask-nextflow/nextflow-hpc.md
skills/prefect-dask-nextflow/prefect-dask.md
skills/prefect-dask-nextflow/prefect-hpc-slurm.md
skills/prefect-dask-nextflow/licenses/omics/LICENSE
skills/prefect-dask-nextflow/scripts/submit_nextflow.sh
skills/prefect-dask-nextflow/templates/nextflow-run.sbatch
skills/prepare-rare-disease-case/DNAKIT.md
skills/prepare-rare-disease-case/SKILL.md
skills/prepare-rare-disease-case/UPSTREAM.md
skills/prepare-rare-disease-case/agents/openai.yaml
skills/prepare-rare-disease-case/licenses/genetic-counseling/LICENSE
skills/prepare-rare-disease-case/references/case-preparation.md
skills/primer-design-primer-basics/DNAKIT.md
skills/primer-design-primer-basics/SKILL.md
skills/primer-design-primer-basics/UPSTREAM.md
skills/primer-design-primer-basics/usage-guide.md
skills/primer-design-primer-basics/examples/primer_design.py
skills/primer-design-primer-basics/licenses/bioskills/LICENSE
skills/primer-design-primer-specificity/DNAKIT.md
skills/primer-design-primer-specificity/SKILL.md
skills/primer-design-primer-specificity/UPSTREAM.md
skills/primer-design-primer-specificity/usage-guide.md
skills/primer-design-primer-specificity/examples/three_prime_anchor.py
skills/primer-design-primer-specificity/licenses/bioskills/LICENSE
skills/primer-design-primer-validation/DNAKIT.md
skills/primer-design-primer-validation/SKILL.md
skills/primer-design-primer-validation/UPSTREAM.md
skills/primer-design-primer-validation/usage-guide.md
skills/primer-design-primer-validation/examples/validate_primers.py
skills/primer-design-primer-validation/licenses/bioskills/LICENSE
skills/primer-design-qpcr-primers/DNAKIT.md
skills/primer-design-qpcr-primers/SKILL.md
skills/primer-design-qpcr-primers/UPSTREAM.md
skills/primer-design-qpcr-primers/usage-guide.md
skills/primer-design-qpcr-primers/examples/qpcr_design.py
skills/primer-design-qpcr-primers/licenses/bioskills/LICENSE
skills/progenomes/DNAKIT.md
skills/progenomes/SKILL.md
skills/progenomes/UPSTREAM.md
skills/progenomes/licenses/pku-metagenomics/LICENSE
skills/progenomes/references/upstream-docs/compute-setup.md
skills/progenomes/references/upstream-docs/getting-started.md
skills/progenomes/references/upstream-docs/multi-platform.md
skills/progenomes/references/upstream-docs/public-databases.md
skills/progenomes/references/upstream-docs/references.md
skills/progenomes/references/upstream-docs/skills.md
skills/progenomes/references/upstream-docs/standard-pipeline.md
skills/progenomes/references/upstream-docs/tool-selection.md
skills/progenomes/references/upstream-docs/troubleshooting.md
skills/protein-lof-mechanism/DNAKIT.md
skills/protein-lof-mechanism/SKILL.md
skills/protein-lof-mechanism/UPSTREAM.md
skills/protein-lof-mechanism/licenses/tooluniverse/LICENSE
skills/protein-sae-variant-interpretation/DNAKIT.md
skills/protein-sae-variant-interpretation/SKILL.md
skills/protein-sae-variant-interpretation/UPSTREAM.md
skills/protein-sae-variant-interpretation/licenses/tooluniverse/LICENSE
skills/prs/DNAKIT.md
skills/prs/LICENSE
skills/prs/SKILL.md
skills/prs/UPSTREAM.md
skills/prs/references/COJO_FORMAT.md
skills/prs/references/SBAYESRC.md
skills/prs/references/upstream-readme.md
skills/prs/scripts/prs.py
skills/prs/scripts/sbayesrc_run.R
skills/pysam/DNAKIT.md
skills/pysam/SKILL.md
skills/pysam/UPSTREAM.md
skills/pysam/licenses/kdense/CITATION.cff
skills/pysam/licenses/kdense/LICENSE.md
skills/pysam/references/alignment_files.md
skills/pysam/references/api_reference.md
skills/pysam/references/common_workflows.md
skills/pysam/references/coordinates_and_indexing.md
skills/pysam/references/cram_and_performance.md
skills/pysam/references/migration_to_0_24.md
skills/pysam/references/sequence_files.md
skills/pysam/references/sources.md
skills/pysam/references/variant_files.md
skills/pysam/scripts/alignment_qc.py
skills/pysam/scripts/filter_alignments.py
skills/pysam/scripts/inspect_hts.py
skills/pysam/scripts/variant_summary.py
skills/qsap/DNAKIT.md
skills/qsap/SKILL.md
skills/qsap/UPSTREAM.md
skills/qsap/licenses/pku-metagenomics/LICENSE
skills/qsap/references/upstream-docs/compute-setup.md
skills/qsap/references/upstream-docs/getting-started.md
skills/qsap/references/upstream-docs/multi-platform.md
skills/qsap/references/upstream-docs/public-databases.md
skills/qsap/references/upstream-docs/references.md
skills/qsap/references/upstream-docs/skills.md
skills/qsap/references/upstream-docs/standard-pipeline.md
skills/qsap/references/upstream-docs/tool-selection.md
skills/qsap/references/upstream-docs/troubleshooting.md
skills/qtl-candidate-gene/CITATION.cff
skills/qtl-candidate-gene/DNAKIT.md
skills/qtl-candidate-gene/EXAMPLE.md
skills/qtl-candidate-gene/LICENSE
skills/qtl-candidate-gene/SKILL.md
skills/qtl-candidate-gene/UPSTREAM.md
skills/qtl-candidate-gene/requirements.txt
skills/qtl-candidate-gene/data/AccessionRename.txt
skills/qtl-candidate-gene/data/ITAG4.1_EB_regions.gff3
skills/qtl-candidate-gene/references/data-sources.md
skills/qtl-candidate-gene/references/interpretation-guide.md
skills/qtl-candidate-gene/references/upstream-readme.md
skills/qtl-candidate-gene/scripts/cite_support.py
skills/qtl-candidate-gene/scripts/diagnostic_variants.py
skills/qtl-candidate-gene/scripts/gene_function.py
skills/qtl-candidate-gene/scripts/genes_in_interval.py
skills/qtl-candidate-gene/scripts/pubmed.py
skills/qtl-candidate-gene/scripts/verify_report.py
skills/quality-assessment/DNAKIT.md
skills/quality-assessment/SKILL.md
skills/quality-assessment/UPSTREAM.md
skills/quality-assessment/licenses/encode-toolkit/CITATION.cff
skills/quality-assessment/licenses/encode-toolkit/LICENSE
skills/quality-assessment/references/literature.md
skills/rare-disease-diagnosis/CHECKLIST.md
skills/rare-disease-diagnosis/DIAGNOSTIC_WORKFLOW.md
skills/rare-disease-diagnosis/DNAKIT.md
skills/rare-disease-diagnosis/EXAMPLES.md
skills/rare-disease-diagnosis/REPORT_TEMPLATE.md
skills/rare-disease-diagnosis/SKILL.md
skills/rare-disease-diagnosis/TOOLS_REFERENCE.md
skills/rare-disease-diagnosis/UPSTREAM.md
skills/rare-disease-diagnosis/licenses/tooluniverse/LICENSE
skills/rare-disease-diagnosis/scripts/clinical_patterns.py
skills/rare-disease-genomics/DNAKIT.md
skills/rare-disease-genomics/SKILL.md
skills/rare-disease-genomics/UPSTREAM.md
skills/rare-disease-genomics/licenses/tooluniverse/LICENSE
skills/rare-high-impact-variants/DNAKIT.md
skills/rare-high-impact-variants/SKILL.md
skills/rare-high-impact-variants/UPSTREAM.md
skills/rare-high-impact-variants/api.py
skills/rare-high-impact-variants/demo_input.txt
skills/rare-high-impact-variants/rare_high_impact_variants.py
skills/rare-high-impact-variants/bench_test_cases/rhi_01_basic_correct/ground_truth.txt
skills/rare-high-impact-variants/bench_test_cases/rhi_01_basic_correct/input.txt
skills/rare-high-impact-variants/bench_test_cases/rhi_02_empty_input/ground_truth.txt
skills/rare-high-impact-variants/bench_test_cases/rhi_02_empty_input/input.txt
skills/rare-high-impact-variants/bench_test_cases/rhi_03_malformed_input/ground_truth.txt
skills/rare-high-impact-variants/bench_test_cases/rhi_03_malformed_input/input.txt
skills/rare-high-impact-variants/licenses/clawbio/CITATION.cff
skills/rare-high-impact-variants/licenses/clawbio/LICENSE
skills/rare-high-impact-variants/tests/test_logic.py
skills/rare-high-impact-variants/tests/test_rare_high_impact_variants.py
skills/read-alignment-bowtie2-alignment/DNAKIT.md
skills/read-alignment-bowtie2-alignment/SKILL.md
skills/read-alignment-bowtie2-alignment/UPSTREAM.md
skills/read-alignment-bowtie2-alignment/usage-guide.md
skills/read-alignment-bowtie2-alignment/examples/align_bowtie2.sh
skills/read-alignment-bowtie2-alignment/licenses/bioskills/LICENSE
skills/read-alignment-bwa-alignment/DNAKIT.md
skills/read-alignment-bwa-alignment/SKILL.md
skills/read-alignment-bwa-alignment/UPSTREAM.md
skills/read-alignment-bwa-alignment/usage-guide.md
skills/read-alignment-bwa-alignment/examples/align_bwa.sh
skills/read-alignment-bwa-alignment/licenses/bioskills/LICENSE
skills/read-qc-adapter-trimming/DNAKIT.md
skills/read-qc-adapter-trimming/SKILL.md
skills/read-qc-adapter-trimming/UPSTREAM.md
skills/read-qc-adapter-trimming/usage-guide.md
skills/read-qc-adapter-trimming/examples/trim_adapters.sh
skills/read-qc-adapter-trimming/licenses/bioskills/LICENSE
skills/read-qc-contamination-screening/DNAKIT.md
skills/read-qc-contamination-screening/SKILL.md
skills/read-qc-contamination-screening/UPSTREAM.md
skills/read-qc-contamination-screening/usage-guide.md
skills/read-qc-contamination-screening/examples/screen_samples.sh
skills/read-qc-contamination-screening/licenses/bioskills/LICENSE
skills/read-qc-fastp-workflow/DNAKIT.md
skills/read-qc-fastp-workflow/SKILL.md
skills/read-qc-fastp-workflow/UPSTREAM.md
skills/read-qc-fastp-workflow/usage-guide.md
skills/read-qc-fastp-workflow/examples/fastp_pipeline.sh
skills/read-qc-fastp-workflow/licenses/bioskills/LICENSE
skills/read-qc-quality-filtering/DNAKIT.md
skills/read-qc-quality-filtering/SKILL.md
skills/read-qc-quality-filtering/UPSTREAM.md
skills/read-qc-quality-filtering/usage-guide.md
skills/read-qc-quality-filtering/examples/quality_filter.sh
skills/read-qc-quality-filtering/licenses/bioskills/LICENSE
skills/read-qc-quality-reports/DNAKIT.md
skills/read-qc-quality-reports/SKILL.md
skills/read-qc-quality-reports/UPSTREAM.md
skills/read-qc-quality-reports/usage-guide.md
skills/read-qc-quality-reports/examples/run_qc_pipeline.sh
skills/read-qc-quality-reports/licenses/bioskills/LICENSE
skills/read-qc-umi-processing/DNAKIT.md
skills/read-qc-umi-processing/SKILL.md
skills/read-qc-umi-processing/UPSTREAM.md
skills/read-qc-umi-processing/usage-guide.md
skills/read-qc-umi-processing/examples/umi_workflow.sh
skills/read-qc-umi-processing/licenses/bioskills/LICENSE
skills/read-sequences/DNAKIT.md
skills/read-sequences/SKILL.md
skills/read-sequences/UPSTREAM.md
skills/read-sequences/tests.json
skills/read-sequences/usage-guide.md
skills/read-sequences/examples/access_patterns.py
skills/read-sequences/examples/basic_parsing.py
skills/read-sequences/examples/fastq_quality.py
skills/read-sequences/examples/genbank_features.py
skills/read-sequences/examples/random_access.py
skills/read-sequences/examples/sample.fasta
skills/read-sequences/examples/sample.fastq
skills/read-sequences/examples/sample.gb
skills/read-sequences/examples/single.fasta
skills/read-sequences/licenses/bioskills/LICENSE
skills/recombinator/DNAKIT.md
skills/recombinator/SKILL.md
skills/recombinator/UPSTREAM.md
skills/recombinator/recombinator.py
skills/recombinator/licenses/clawbio/CITATION.cff
skills/recombinator/licenses/clawbio/LICENSE
skills/reference-operations/DNAKIT.md
skills/reference-operations/SKILL.md
skills/reference-operations/UPSTREAM.md
skills/reference-operations/usage-guide.md
skills/reference-operations/examples/prepare_reference.sh
skills/reference-operations/licenses/bioskills/LICENSE
skills/regulatory-elements/DNAKIT.md
skills/regulatory-elements/SKILL.md
skills/regulatory-elements/UPSTREAM.md
skills/regulatory-elements/licenses/encode-toolkit/CITATION.cff
skills/regulatory-elements/licenses/encode-toolkit/LICENSE
skills/regulatory-elements/references/literature.md
skills/regulatory-genomics/DNAKIT.md
skills/regulatory-genomics/SKILL.md
skills/regulatory-genomics/UPSTREAM.md
skills/regulatory-genomics/licenses/tooluniverse/LICENSE
skills/regulatory-variant-analysis/DNAKIT.md
skills/regulatory-variant-analysis/SKILL.md
skills/regulatory-variant-analysis/UPSTREAM.md
skills/regulatory-variant-analysis/licenses/tooluniverse/LICENSE
skills/regulomedb-database/DNAKIT.md
skills/regulomedb-database/SKILL.md
skills/regulomedb-database/UPSTREAM.md
skills/regulomedb-database/licenses/kdense/CITATION.cff
skills/regulomedb-database/licenses/kdense/LICENSE.md
skills/regulomedb-database/licenses/sciagent/CC-BY-4.0.txt
skills/regulomedb-database/licenses/sciagent/LICENSE
skills/regulomedb-database/licenses/tooluniverse/LICENSE
skills/remap-database/DNAKIT.md
skills/remap-database/SKILL.md
skills/remap-database/UPSTREAM.md
skills/remap-database/licenses/kdense/CITATION.cff
skills/remap-database/licenses/kdense/LICENSE.md
skills/remap-database/licenses/sciagent/CC-BY-4.0.txt
skills/remap-database/licenses/sciagent/LICENSE
skills/remap-database/licenses/tooluniverse/LICENSE
skills/restriction-enzyme-selection/DNAKIT.md
skills/restriction-enzyme-selection/SKILL.md
skills/restriction-enzyme-selection/UPSTREAM.md
skills/restriction-enzyme-selection/usage-guide.md
skills/restriction-enzyme-selection/examples/cloning_strategy.py
skills/restriction-enzyme-selection/examples/select_enzymes.py
skills/restriction-enzyme-selection/licenses/bioskills/LICENSE
skills/restriction-fragment-analysis/DNAKIT.md
skills/restriction-fragment-analysis/SKILL.md
skills/restriction-fragment-analysis/UPSTREAM.md
skills/restriction-fragment-analysis/usage-guide.md
skills/restriction-fragment-analysis/examples/gel_simulation.py
skills/restriction-fragment-analysis/examples/predict_fragments.py
skills/restriction-fragment-analysis/licenses/bioskills/LICENSE
skills/restriction-golden-gate-assembly/DNAKIT.md
skills/restriction-golden-gate-assembly/SKILL.md
skills/restriction-golden-gate-assembly/UPSTREAM.md
skills/restriction-golden-gate-assembly/usage-guide.md
skills/restriction-golden-gate-assembly/examples/domestication_check.py
skills/restriction-golden-gate-assembly/examples/overhang_set_validate.py
skills/restriction-golden-gate-assembly/licenses/bioskills/LICENSE
skills/restriction-mapping/DNAKIT.md
skills/restriction-mapping/SKILL.md
skills/restriction-mapping/UPSTREAM.md
skills/restriction-mapping/usage-guide.md
skills/restriction-mapping/examples/create_map.py
skills/restriction-mapping/examples/plasmid_map.py
skills/restriction-mapping/licenses/bioskills/LICENSE
skills/restriction-sites/DNAKIT.md
skills/restriction-sites/SKILL.md
skills/restriction-sites/UPSTREAM.md
skills/restriction-sites/usage-guide.md
skills/restriction-sites/examples/circular_plasmid.py
skills/restriction-sites/examples/find_sites.py
skills/restriction-sites/licenses/bioskills/LICENSE
skills/reverse-complement/DNAKIT.md
skills/reverse-complement/SKILL.md
skills/reverse-complement/UPSTREAM.md
skills/reverse-complement/usage-guide.md
skills/reverse-complement/examples/basic_operations.py
skills/reverse-complement/examples/iupac_and_features.py
skills/reverse-complement/examples/palindrome_check.py
skills/reverse-complement/examples/primer_design.py
skills/reverse-complement/licenses/bioskills/LICENSE
skills/review-variant-table/DNAKIT.md
skills/review-variant-table/SKILL.md
skills/review-variant-table/UPSTREAM.md
skills/review-variant-table/agents/openai.yaml
skills/review-variant-table/licenses/genetic-counseling/LICENSE
skills/review-variant-table/references/variant-table-guardrails.md
skills/review-variant-table/scripts/review_variant_table.py
skills/sam-bam-basics/DNAKIT.md
skills/sam-bam-basics/SKILL.md
skills/sam-bam-basics/UPSTREAM.md
skills/sam-bam-basics/usage-guide.md
skills/sam-bam-basics/examples/convert_formats.sh
skills/sam-bam-basics/examples/view_bam.py
skills/sam-bam-basics/licenses/bioskills/LICENSE
skills/sample-qc-triage/DNAKIT.md
skills/sample-qc-triage/SKILL.md
skills/sample-qc-triage/UPSTREAM.md
skills/sample-qc-triage/demo_qc_metrics.csv
skills/sample-qc-triage/sample_qc_triage.py
skills/sample-qc-triage/licenses/clawbio/CITATION.cff
skills/sample-qc-triage/licenses/clawbio/LICENSE
skills/sample-qc-triage/tests/test_sample_qc_triage.py
skills/samtools-bam-processing/DNAKIT.md
skills/samtools-bam-processing/SKILL.md
skills/samtools-bam-processing/UPSTREAM.md
skills/samtools-bam-processing/licenses/kdense/CITATION.cff
skills/samtools-bam-processing/licenses/kdense/LICENSE.md
skills/samtools-bam-processing/licenses/sciagent/CC-BY-4.0.txt
skills/samtools-bam-processing/licenses/sciagent/LICENSE
skills/samtools-bam-processing/licenses/tooluniverse/LICENSE
skills/scikit-bio/DNAKIT.md
skills/scikit-bio/SKILL.md
skills/scikit-bio/UPSTREAM.md
skills/scikit-bio/licenses/kdense/CITATION.cff
skills/scikit-bio/licenses/kdense/LICENSE.md
skills/scikit-bio/licenses/sciagent/CC-BY-4.0.txt
skills/scikit-bio/licenses/sciagent/LICENSE
skills/scikit-bio/licenses/tooluniverse/LICENSE
skills/scikit-bio/references/extended_api.md
skills/scvi-tools/DNAKIT.md
skills/scvi-tools/LICENSE
skills/scvi-tools/LICENSE.txt
skills/scvi-tools/SKILL.md
skills/scvi-tools/UPSTREAM.md
skills/scvi-tools/references/atac_peakvi.md
skills/scvi-tools/references/batch_correction_sysvi.md
skills/scvi-tools/references/citeseq_totalvi.md
skills/scvi-tools/references/data_preparation.md
skills/scvi-tools/references/environment_setup.md
skills/scvi-tools/references/label_transfer.md
skills/scvi-tools/references/multiome_multivi.md
skills/scvi-tools/references/rna_velocity_velovi.md
skills/scvi-tools/references/scarches_mapping.md
skills/scvi-tools/references/scrna_integration.md
skills/scvi-tools/references/spatial_deconvolution.md
skills/scvi-tools/references/troubleshooting.md
skills/scvi-tools/references/upstream-readme.md
skills/scvi-tools/scripts/cluster_embed.py
skills/scvi-tools/scripts/differential_expression.py
skills/scvi-tools/scripts/integrate_datasets.py
skills/scvi-tools/scripts/model_utils.py
skills/scvi-tools/scripts/prepare_data.py
skills/scvi-tools/scripts/train_model.py
skills/scvi-tools/scripts/transfer_labels.py
skills/scvi-tools/scripts/validate_adata.py
skills/seq-objects/DNAKIT.md
skills/seq-objects/SKILL.md
skills/seq-objects/UPSTREAM.md
skills/seq-objects/usage-guide.md
skills/seq-objects/examples/basic_seq.py
skills/seq-objects/examples/seqrecord_annotations.py
skills/seq-objects/licenses/bioskills/LICENSE
skills/seq-wrangler/DNAKIT.md
skills/seq-wrangler/README.md
skills/seq-wrangler/SKILL.md
skills/seq-wrangler/UPSTREAM.md
skills/seq-wrangler/seq_wrangler.py
skills/seq-wrangler/examples/demo-results/report.md
skills/seq-wrangler/licenses/clawbio/CITATION.cff
skills/seq-wrangler/licenses/clawbio/LICENSE
skills/seq-wrangler/tests/test_seq_wrangler.py
skills/sequence-analysis/DNAKIT.md
skills/sequence-analysis/SKILL.md
skills/sequence-analysis/UPSTREAM.md
skills/sequence-analysis/licenses/tooluniverse/LICENSE
skills/sequence-analysis/scripts/amino_acids.py
skills/sequence-analysis/scripts/biology_facts.py
skills/sequence-analysis/scripts/sequence_tools.py
skills/sequence-analysis/scripts/translate_dna.py
skills/sequence-properties/DNAKIT.md
skills/sequence-properties/SKILL.md
skills/sequence-properties/UPSTREAM.md
skills/sequence-properties/usage-guide.md
skills/sequence-properties/examples/advanced_analysis.py
skills/sequence-properties/examples/dna_properties.py
skills/sequence-properties/examples/gc_analysis.py
skills/sequence-properties/examples/property_traps.py
skills/sequence-properties/examples/protein_properties.py
skills/sequence-properties/licenses/bioskills/LICENSE
skills/sequence-retrieval/CHECKLIST.md
skills/sequence-retrieval/DNAKIT.md
skills/sequence-retrieval/SKILL.md
skills/sequence-retrieval/UPSTREAM.md
skills/sequence-retrieval/examples.md
skills/sequence-retrieval/licenses/tooluniverse/LICENSE
skills/sequence-slicing/DNAKIT.md
skills/sequence-slicing/SKILL.md
skills/sequence-slicing/UPSTREAM.md
skills/sequence-slicing/usage-guide.md
skills/sequence-slicing/examples/basic_slicing.py
skills/sequence-slicing/examples/chunking.py
skills/sequence-slicing/examples/concatenation.py
skills/sequence-slicing/examples/seqrecord_slicing.py
skills/sequence-slicing/licenses/bioskills/LICENSE
skills/sequence-statistics/DNAKIT.md
skills/sequence-statistics/SKILL.md
skills/sequence-statistics/UPSTREAM.md
skills/sequence-statistics/usage-guide.md
skills/sequence-statistics/examples/seq_stats.py
skills/sequence-statistics/licenses/bioskills/LICENSE
skills/single-cell-clustering/DNAKIT.md
skills/single-cell-clustering/SKILL.md
skills/single-cell-clustering/UPSTREAM.md
skills/single-cell-clustering/usage-guide.md
skills/single-cell-clustering/examples/cluster_scanpy.py
skills/single-cell-clustering/examples/cluster_seurat.R
skills/single-cell-clustering/licenses/bioskills/LICENSE
skills/single-cell-cnv-inference/DNAKIT.md
skills/single-cell-cnv-inference/LICENSE
skills/single-cell-cnv-inference/SKILL.md
skills/single-cell-cnv-inference/UPSTREAM.md
skills/single-cell-cnv-inference/usage-guide.md
skills/single-cell-cnv-inference/examples/infercnv_malignant_calling.R
skills/single-cell-cnv-inference/references/upstream-readme.md
skills/single-cell-data-io/DNAKIT.md
skills/single-cell-data-io/SKILL.md
skills/single-cell-data-io/UPSTREAM.md
skills/single-cell-data-io/usage-guide.md
skills/single-cell-data-io/examples/load_10x_scanpy.py
skills/single-cell-data-io/examples/load_10x_seurat.R
skills/single-cell-data-io/licenses/bioskills/LICENSE
skills/single-cell-lineage-tracing/DNAKIT.md
skills/single-cell-lineage-tracing/SKILL.md
skills/single-cell-lineage-tracing/UPSTREAM.md
skills/single-cell-lineage-tracing/usage-guide.md
skills/single-cell-lineage-tracing/examples/cassiopeia_reconstruction.py
skills/single-cell-lineage-tracing/examples/cospar_dynamics.py
skills/single-cell-lineage-tracing/licenses/bioskills/LICENSE
skills/single-cell-multimodal-integration/DNAKIT.md
skills/single-cell-multimodal-integration/SKILL.md
skills/single-cell-multimodal-integration/UPSTREAM.md
skills/single-cell-multimodal-integration/usage-guide.md
skills/single-cell-multimodal-integration/examples/cite_seq_analysis.R
skills/single-cell-multimodal-integration/examples/cite_seq_analysis.py
skills/single-cell-multimodal-integration/licenses/bioskills/LICENSE
skills/single-cell-preprocessing/DNAKIT.md
skills/single-cell-preprocessing/SKILL.md
skills/single-cell-preprocessing/UPSTREAM.md
skills/single-cell-preprocessing/usage-guide.md
skills/single-cell-preprocessing/examples/preprocess_scanpy.py
skills/single-cell-preprocessing/examples/preprocess_seurat.R
skills/single-cell-preprocessing/licenses/bioskills/LICENSE
skills/singlem/DNAKIT.md
skills/singlem/SKILL.md
skills/singlem/UPSTREAM.md
skills/singlem/licenses/pku-metagenomics/LICENSE
skills/singlem/references/upstream-docs/compute-setup.md
skills/singlem/references/upstream-docs/getting-started.md
skills/singlem/references/upstream-docs/multi-platform.md
skills/singlem/references/upstream-docs/public-databases.md
skills/singlem/references/upstream-docs/references.md
skills/singlem/references/upstream-docs/skills.md
skills/singlem/references/upstream-docs/standard-pipeline.md
skills/singlem/references/upstream-docs/tool-selection.md
skills/singlem/references/upstream-docs/troubleshooting.md
skills/spacedust/DNAKIT.md
skills/spacedust/SKILL.md
skills/spacedust/UPSTREAM.md
skills/spacedust/licenses/pku-metagenomics/LICENSE
skills/spacedust/references/upstream-docs/compute-setup.md
skills/spacedust/references/upstream-docs/getting-started.md
skills/spacedust/references/upstream-docs/multi-platform.md
skills/spacedust/references/upstream-docs/public-databases.md
skills/spacedust/references/upstream-docs/references.md
skills/spacedust/references/upstream-docs/skills.md
skills/spacedust/references/upstream-docs/standard-pipeline.md
skills/spacedust/references/upstream-docs/tool-selection.md
skills/spacedust/references/upstream-docs/troubleshooting.md
skills/splice-variant-prediction/DNAKIT.md
skills/splice-variant-prediction/SKILL.md
skills/splice-variant-prediction/UPSTREAM.md
skills/splice-variant-prediction/usage-guide.md
skills/splice-variant-prediction/examples/spliceai_clingen_classify.py
skills/splice-variant-prediction/licenses/bioskills/LICENSE
skills/sra-data/DNAKIT.md
skills/sra-data/SKILL.md
skills/sra-data/UPSTREAM.md
skills/sra-data/usage-guide.md
skills/sra-data/examples/download_batch.sh
skills/sra-data/examples/download_single.sh
skills/sra-data/examples/find_sra_runs.py
skills/sra-data/examples/prefetch_large.sh
skills/sra-data/licenses/bioskills/LICENSE
skills/systems-biology-gene-essentiality/DNAKIT.md
skills/systems-biology-gene-essentiality/SKILL.md
skills/systems-biology-gene-essentiality/UPSTREAM.md
skills/systems-biology-gene-essentiality/usage-guide.md
skills/systems-biology-gene-essentiality/examples/gene_essentiality.py
skills/systems-biology-gene-essentiality/licenses/bioskills/LICENSE
skills/systems-biology-metabolic-reconstruction/DNAKIT.md
skills/systems-biology-metabolic-reconstruction/SKILL.md
skills/systems-biology-metabolic-reconstruction/UPSTREAM.md
skills/systems-biology-metabolic-reconstruction/usage-guide.md
skills/systems-biology-metabolic-reconstruction/examples/model_reconstruction.py
skills/systems-biology-metabolic-reconstruction/licenses/bioskills/LICENSE
skills/tangermeme/DNAKIT.md
skills/tangermeme/LICENSE
skills/tangermeme/SKILL.md
skills/tangermeme/UPSTREAM.md
skills/tangermeme/references/annotate.md
skills/tangermeme/references/comparing-models.md
skills/tangermeme/references/deep_lift_shap.md
skills/tangermeme/references/design.md
skills/tangermeme/references/func-pattern.md
skills/tangermeme/references/io-loci.md
skills/tangermeme/references/model-wrapping.md
skills/tangermeme/references/motif-effects.md
skills/tangermeme/references/notebook-walkthrough.md
skills/tangermeme/references/plot.md
skills/tangermeme/references/product.md
skills/tangermeme/references/saturation_mutagenesis.md
skills/tangermeme/references/seqlets.md
skills/tangermeme/references/upstream-readme.md
skills/tangermeme/references/variant-effect.md
skills/taxvamb/DNAKIT.md
skills/taxvamb/SKILL.md
skills/taxvamb/UPSTREAM.md
skills/taxvamb/licenses/pku-metagenomics/LICENSE
skills/taxvamb/references/upstream-docs/compute-setup.md
skills/taxvamb/references/upstream-docs/getting-started.md
skills/taxvamb/references/upstream-docs/multi-platform.md
skills/taxvamb/references/upstream-docs/public-databases.md
skills/taxvamb/references/upstream-docs/references.md
skills/taxvamb/references/upstream-docs/skills.md
skills/taxvamb/references/upstream-docs/standard-pipeline.md
skills/taxvamb/references/upstream-docs/tool-selection.md
skills/taxvamb/references/upstream-docs/troubleshooting.md
skills/tcr-bcr-analysis-immcantation-analysis/DNAKIT.md
skills/tcr-bcr-analysis-immcantation-analysis/SKILL.md
skills/tcr-bcr-analysis-immcantation-analysis/UPSTREAM.md
skills/tcr-bcr-analysis-immcantation-analysis/usage-guide.md
skills/tcr-bcr-analysis-immcantation-analysis/examples/bcr_analysis.R
skills/tcr-bcr-analysis-immcantation-analysis/licenses/bioskills/LICENSE
skills/tcr-bcr-analysis-mixcr-analysis/DNAKIT.md
skills/tcr-bcr-analysis-mixcr-analysis/SKILL.md
skills/tcr-bcr-analysis-mixcr-analysis/UPSTREAM.md
skills/tcr-bcr-analysis-mixcr-analysis/usage-guide.md
skills/tcr-bcr-analysis-mixcr-analysis/examples/mixcr_workflow.sh
skills/tcr-bcr-analysis-mixcr-analysis/licenses/bioskills/LICENSE
skills/tcr-bcr-analysis-repertoire-visualization/DNAKIT.md
skills/tcr-bcr-analysis-repertoire-visualization/SKILL.md
skills/tcr-bcr-analysis-repertoire-visualization/UPSTREAM.md
skills/tcr-bcr-analysis-repertoire-visualization/usage-guide.md
skills/tcr-bcr-analysis-repertoire-visualization/examples/repertoire_plots.py
skills/tcr-bcr-analysis-repertoire-visualization/licenses/bioskills/LICENSE
skills/tcr-bcr-analysis-scirpy-analysis/DNAKIT.md
skills/tcr-bcr-analysis-scirpy-analysis/SKILL.md
skills/tcr-bcr-analysis-scirpy-analysis/UPSTREAM.md
skills/tcr-bcr-analysis-scirpy-analysis/usage-guide.md
skills/tcr-bcr-analysis-scirpy-analysis/examples/scirpy_integration.py
skills/tcr-bcr-analysis-scirpy-analysis/licenses/bioskills/LICENSE
skills/tcr-bcr-analysis-specificity-annotation/DNAKIT.md
skills/tcr-bcr-analysis-specificity-annotation/SKILL.md
skills/tcr-bcr-analysis-specificity-annotation/UPSTREAM.md
skills/tcr-bcr-analysis-specificity-annotation/usage-guide.md
skills/tcr-bcr-analysis-specificity-annotation/examples/specificity_annotation.py
skills/tcr-bcr-analysis-specificity-annotation/licenses/bioskills/LICENSE
skills/tcr-bcr-analysis-vdjtools-analysis/DNAKIT.md
skills/tcr-bcr-analysis-vdjtools-analysis/SKILL.md
skills/tcr-bcr-analysis-vdjtools-analysis/UPSTREAM.md
skills/tcr-bcr-analysis-vdjtools-analysis/usage-guide.md
skills/tcr-bcr-analysis-vdjtools-analysis/examples/diversity_analysis.sh
skills/tcr-bcr-analysis-vdjtools-analysis/licenses/bioskills/LICENSE
skills/tiledbvcf/DNAKIT.md
skills/tiledbvcf/SKILL.md
skills/tiledbvcf/UPSTREAM.md
skills/tiledbvcf/licenses/kdense/CITATION.cff
skills/tiledbvcf/licenses/kdense/LICENSE.md
skills/track-experiments/DNAKIT.md
skills/track-experiments/SKILL.md
skills/track-experiments/UPSTREAM.md
skills/track-experiments/licenses/encode-toolkit/CITATION.cff
skills/track-experiments/licenses/encode-toolkit/LICENSE
skills/track-experiments/references/literature.md
skills/tracking-taxonomy-updates/DNAKIT.md
skills/tracking-taxonomy-updates/SKILL.md
skills/tracking-taxonomy-updates/UPSTREAM.md
skills/tracking-taxonomy-updates/fixtures/quickclade-machine.tsv
skills/tracking-taxonomy-updates/licenses/omics/LICENSE
skills/tracking-taxonomy-updates/reference/last-verified-snapshots.md
skills/tracking-taxonomy-updates/reference/qa-checklist.md
skills/tracking-taxonomy-updates/reference/ranks-and-identifiers.md
skills/tracking-taxonomy-updates/reference/report-template.md
skills/tracking-taxonomy-updates/reference/sources.md
skills/tracking-taxonomy-updates/reference/tools.md
skills/tracking-taxonomy-updates/scripts/quickclade_to_routing.py
skills/tracking-taxonomy-updates/scripts/submit_taxonomy.sh
skills/tracking-taxonomy-updates/templates/taxonomy-tool.sbatch
skills/transcription-translation/DNAKIT.md
skills/transcription-translation/SKILL.md
skills/transcription-translation/UPSTREAM.md
skills/transcription-translation/usage-guide.md
skills/transcription-translation/examples/basic_conversion.py
skills/transcription-translation/examples/codon_tables.py
skills/transcription-translation/examples/orf_finding.py
skills/transcription-translation/licenses/bioskills/LICENSE
skills/tumor-fraction-estimation/DNAKIT.md
skills/tumor-fraction-estimation/SKILL.md
skills/tumor-fraction-estimation/UPSTREAM.md
skills/tumor-fraction-estimation/usage-guide.md
skills/tumor-fraction-estimation/examples/estimate_tumor_fraction.R
skills/tumor-fraction-estimation/licenses/bioskills/LICENSE
skills/twas/DNAKIT.md
skills/twas/LICENSE
skills/twas/SKILL.md
skills/twas/UPSTREAM.md
skills/twas/references/FUSION.md
skills/twas/references/upstream-readme.md
skills/twas/scripts/twas.py
skills/twas/scripts/twas_run.R
skills/ucsc-conservation-and-tfbs/DNAKIT.md
skills/ucsc-conservation-and-tfbs/SKILL.md
skills/ucsc-conservation-and-tfbs/UPSTREAM.md
skills/ucsc-conservation-and-tfbs/licenses/deepmind/CC-BY-4.0.txt
skills/ucsc-conservation-and-tfbs/licenses/deepmind/LICENSE
skills/ucsc-conservation-and-tfbs/licenses/deepmind/README.md
skills/ucsc-conservation-and-tfbs/licenses/deepmind/SKILL_LICENSES.md
skills/ucsc-conservation-and-tfbs/references/citation.bib
skills/ucsc-conservation-and-tfbs/scripts/get_conservation.py
skills/ucsc-conservation-and-tfbs/scripts/get_tfbs.py
skills/ucsc-conservation-and-tfbs/scripts/list_tracks.py
skills/ucsc-genome-browser/DNAKIT.md
skills/ucsc-genome-browser/SKILL.md
skills/ucsc-genome-browser/UPSTREAM.md
skills/ucsc-genome-browser/licenses/kdense/CITATION.cff
skills/ucsc-genome-browser/licenses/kdense/LICENSE.md
skills/ucsc-genome-browser/licenses/sciagent/CC-BY-4.0.txt
skills/ucsc-genome-browser/licenses/sciagent/LICENSE
skills/ucsc-genome-browser/licenses/tooluniverse/LICENSE
skills/ukb-ppp-region-fetch/.gitignore
skills/ukb-ppp-region-fetch/DNAKIT.md
skills/ukb-ppp-region-fetch/LICENSE
skills/ukb-ppp-region-fetch/SKILL.md
skills/ukb-ppp-region-fetch/UPSTREAM.md
skills/ukb-ppp-region-fetch/environment.yml
skills/ukb-ppp-region-fetch/ukb_ppp_region_fetch.py
skills/ukb-ppp-region-fetch/bundled_slices/README.md
skills/ukb-ppp-region-fetch/bundled_slices/SORT1__EUR__chr1__108774968_109774968.json.gz
skills/ukb-ppp-region-fetch/examples/default.json
skills/ukb-ppp-region-fetch/examples/expected_output.md
skills/ukb-ppp-region-fetch/examples/sort1_ukb_ppp_eur.json
skills/ukb-ppp-region-fetch/references/upstream-readme.md
skills/ukb-ppp-region-fetch/tests/conftest.py
skills/ukb-ppp-region-fetch/tests/test_live_ukb_ppp_region_fetch.py
skills/ukb-ppp-region-fetch/tests/test_ukb_ppp_region_fetch.py
skills/unibind-database/DNAKIT.md
skills/unibind-database/SKILL.md
skills/unibind-database/UPSTREAM.md
skills/unibind-database/licenses/deepmind/CC-BY-4.0.txt
skills/unibind-database/licenses/deepmind/LICENSE
skills/unibind-database/licenses/deepmind/README.md
skills/unibind-database/licenses/deepmind/SKILL_LICENSES.md
skills/unibind-database/references/citation.bib
skills/unibind-database/scripts/unibind_api.py
skills/unicore/DNAKIT.md
skills/unicore/SKILL.md
skills/unicore/UPSTREAM.md
skills/unicore/licenses/pku-metagenomics/LICENSE
skills/unicore/references/upstream-docs/compute-setup.md
skills/unicore/references/upstream-docs/getting-started.md
skills/unicore/references/upstream-docs/multi-platform.md
skills/unicore/references/upstream-docs/public-databases.md
skills/unicore/references/upstream-docs/references.md
skills/unicore/references/upstream-docs/skills.md
skills/unicore/references/upstream-docs/standard-pipeline.md
skills/unicore/references/upstream-docs/tool-selection.md
skills/unicore/references/upstream-docs/troubleshooting.md
skills/variant-analysis/.env.template
skills/variant-analysis/DNAKIT.md
skills/variant-analysis/QUICK_START.md
skills/variant-analysis/SKILL.md
skills/variant-analysis/UPSTREAM.md
skills/variant-analysis/python_implementation.py
skills/variant-analysis/test_variant_analysis.py
skills/variant-analysis/licenses/tooluniverse/LICENSE
skills/variant-analysis/references/annotation_guide.md
skills/variant-analysis/references/mutation_classification_guide.md
skills/variant-analysis/references/sv_cnv_analysis.md
skills/variant-analysis/references/vcf_filtering.md
skills/variant-analysis/scripts/annotate_variants.py
skills/variant-analysis/scripts/coding_variant_filter.py
skills/variant-analysis/scripts/filter_variants.py
skills/variant-analysis/scripts/gatk_haplotypecaller_pipeline.py
skills/variant-analysis/scripts/parse_vcf.py
skills/variant-analysis/scripts/variant_fraction.py
skills/variant-analysis/test_data/cohort2.vcf
skills/variant-analysis/test_data/sample.vcf
skills/variant-annotate/DNAKIT.md
skills/variant-annotate/LICENSE
skills/variant-annotate/SKILL.md
skills/variant-annotate/UPSTREAM.md
skills/variant-annotate/references/upstream-readme.md
skills/variant-annotate/scripts/annotate.py
skills/variant-annotation/DNAKIT.md
skills/variant-annotation/SKILL.md
skills/variant-annotation/UPSTREAM.md
skills/variant-annotation/usage-guide.md
skills/variant-annotation/examples/annotate_vcf.sh
skills/variant-annotation/licenses/bioskills/LICENSE
skills/variant-calling/DNAKIT.md
skills/variant-calling/SKILL.md
skills/variant-calling/UPSTREAM.md
skills/variant-calling/usage-guide.md
skills/variant-calling-deepvariant/DNAKIT.md
skills/variant-calling-deepvariant/SKILL.md
skills/variant-calling-deepvariant/UPSTREAM.md
skills/variant-calling-deepvariant/usage-guide.md
skills/variant-calling-deepvariant/examples/run_deepvariant.sh
skills/variant-calling-deepvariant/licenses/bioskills/LICENSE
skills/variant-calling-filtering-best-practices/DNAKIT.md
skills/variant-calling-filtering-best-practices/SKILL.md
skills/variant-calling-filtering-best-practices/UPSTREAM.md
skills/variant-calling-filtering-best-practices/usage-guide.md
skills/variant-calling-filtering-best-practices/examples/filter_variants.sh
skills/variant-calling-filtering-best-practices/licenses/bioskills/LICENSE
skills/variant-calling-joint-calling/DNAKIT.md
skills/variant-calling-joint-calling/SKILL.md
skills/variant-calling-joint-calling/UPSTREAM.md
skills/variant-calling-joint-calling/usage-guide.md
skills/variant-calling-joint-calling/examples/joint_calling_gatk.sh
skills/variant-calling-joint-calling/licenses/bioskills/LICENSE
skills/variant-calling-structural-variant-calling/DNAKIT.md
skills/variant-calling-structural-variant-calling/SKILL.md
skills/variant-calling-structural-variant-calling/UPSTREAM.md
skills/variant-calling-structural-variant-calling/usage-guide.md
skills/variant-calling-structural-variant-calling/examples/call_svs.sh
skills/variant-calling-structural-variant-calling/examples/svlen_sign_filter.py
skills/variant-calling-structural-variant-calling/licenses/bioskills/LICENSE
skills/variant-calling/examples/call_variants.sh
skills/variant-calling/licenses/bioskills/LICENSE
skills/variant-interpretation/ACMG_CLASSIFICATION.md
skills/variant-interpretation/CHECKLIST.md
skills/variant-interpretation/CODE_PATTERNS.md
skills/variant-interpretation/DNAKIT.md
skills/variant-interpretation/EXAMPLES.md
skills/variant-interpretation/SKILL.md
skills/variant-interpretation/TOOLS_REFERENCE.md
skills/variant-interpretation/UPSTREAM.md
skills/variant-interpretation/licenses/tooluniverse/LICENSE
skills/variant-normalization/DNAKIT.md
skills/variant-normalization/SKILL.md
skills/variant-normalization/UPSTREAM.md
skills/variant-normalization/usage-guide.md
skills/variant-normalization/examples/normalize_vcf.sh
skills/variant-normalization/licenses/bioskills/LICENSE
skills/variant-predictor-dms-validation/DNAKIT.md
skills/variant-predictor-dms-validation/SKILL.md
skills/variant-predictor-dms-validation/UPSTREAM.md
skills/variant-predictor-dms-validation/licenses/tooluniverse/LICENSE
skills/variant-to-mechanism/DNAKIT.md
skills/variant-to-mechanism/SKILL.md
skills/variant-to-mechanism/UPSTREAM.md
skills/variant-to-mechanism/licenses/tooluniverse/LICENSE
skills/vcf-basics/DNAKIT.md
skills/vcf-basics/SKILL.md
skills/vcf-basics/UPSTREAM.md
skills/vcf-basics/usage-guide.md
skills/vcf-basics/examples/view_vcf.py
skills/vcf-basics/licenses/bioskills/LICENSE
skills/vcf-manipulation/DNAKIT.md
skills/vcf-manipulation/SKILL.md
skills/vcf-manipulation/UPSTREAM.md
skills/vcf-manipulation/usage-guide.md
skills/vcf-manipulation/examples/compare_vcfs.sh
skills/vcf-manipulation/licenses/bioskills/LICENSE
skills/vcf-statistics/DNAKIT.md
skills/vcf-statistics/SKILL.md
skills/vcf-statistics/UPSTREAM.md
skills/vcf-statistics/usage-guide.md
skills/vcf-statistics/examples/vcf_stats.py
skills/vcf-statistics/licenses/bioskills/LICENSE
skills/vcontact/DNAKIT.md
skills/vcontact/SKILL.md
skills/vcontact/UPSTREAM.md
skills/vcontact/licenses/pku-metagenomics/LICENSE
skills/vcontact/references/upstream-docs/compute-setup.md
skills/vcontact/references/upstream-docs/getting-started.md
skills/vcontact/references/upstream-docs/multi-platform.md
skills/vcontact/references/upstream-docs/public-databases.md
skills/vcontact/references/upstream-docs/references.md
skills/vcontact/references/upstream-docs/skills.md
skills/vcontact/references/upstream-docs/standard-pipeline.md
skills/vcontact/references/upstream-docs/tool-selection.md
skills/vcontact/references/upstream-docs/troubleshooting.md
skills/viromics/DNAKIT.md
skills/viromics/SKILL.md
skills/viromics/UPSTREAM.md
skills/viromics/docs/README.md
skills/viromics/docs/checkv-usage.md
skills/viromics/docs/genomad-usage.md
skills/viromics/docs/gvclass-usage.md
skills/viromics/docs/vcontact3-usage.md
skills/viromics/fixtures/database.fixture
skills/viromics/fixtures/hypotheses.tsv
skills/viromics/fixtures/metrics.tsv
skills/viromics/fixtures/reflections.tsv
skills/viromics/fixtures/resources.json
skills/viromics/fixtures/comparative/conserved_neighborhoods.tsv
skills/viromics/fixtures/comparative/family_copy_number_comparison.tsv
skills/viromics/fixtures/comparative/marker_census.tsv
skills/viromics/fixtures/comparative/ncRNA_census.tsv
skills/viromics/licenses/omics/LICENSE
skills/viromics/schemas/evidence-bundle.schema.json
skills/viromics/scripts/build_viromics_evidence.py
skills/virulencefinder/DNAKIT.md
skills/virulencefinder/SKILL.md
skills/virulencefinder/UPSTREAM.md
skills/virulencefinder/licenses/pku-metagenomics/LICENSE
skills/virulencefinder/references/upstream-docs/compute-setup.md
skills/virulencefinder/references/upstream-docs/getting-started.md
skills/virulencefinder/references/upstream-docs/multi-platform.md
skills/virulencefinder/references/upstream-docs/public-databases.md
skills/virulencefinder/references/upstream-docs/references.md
skills/virulencefinder/references/upstream-docs/skills.md
skills/virulencefinder/references/upstream-docs/standard-pipeline.md
skills/virulencefinder/references/upstream-docs/tool-selection.md
skills/virulencefinder/references/upstream-docs/troubleshooting.md
skills/vitis-pangenome/DNAKIT.md
skills/vitis-pangenome/SKILL.md
skills/vitis-pangenome/UPSTREAM.md
skills/vitis-pangenome/licenses/plant-skills/LICENSE
skills/vitis-popgen/DNAKIT.md
skills/vitis-popgen/SKILL.md
skills/vitis-popgen/UPSTREAM.md
skills/vitis-popgen/licenses/plant-skills/LICENSE
skills/vitis-te/DNAKIT.md
skills/vitis-te/SKILL.md
skills/vitis-te/UPSTREAM.md
skills/vitis-te/licenses/plant-skills/LICENSE
skills/wgs-prs/DNAKIT.md
skills/wgs-prs/SKILL.md
skills/wgs-prs/UPSTREAM.md
skills/wgs-prs/repro_bundle.py
skills/wgs-prs/wgs_prs.py
skills/wgs-prs/licenses/clawbio/CITATION.cff
skills/wgs-prs/licenses/clawbio/LICENSE
skills/wgs-prs/tests/conftest.py
skills/wgs-prs/tests/test_repro_bundle.py
skills/wgs-prs/tests/test_sarek.py
skills/wgs-prs/tests/test_vcf_qc.py
skills/wgs-prs/tests/test_wgs_prs.py
skills/workflow-management-cwl-workflows/DNAKIT.md
skills/workflow-management-cwl-workflows/SKILL.md
skills/workflow-management-cwl-workflows/UPSTREAM.md
skills/workflow-management-cwl-workflows/usage-guide.md
skills/workflow-management-cwl-workflows/examples/rnaseq.cwl
skills/workflow-management-cwl-workflows/licenses/bioskills/LICENSE
skills/workflow-management-nextflow-pipelines/DNAKIT.md
skills/workflow-management-nextflow-pipelines/SKILL.md
skills/workflow-management-nextflow-pipelines/UPSTREAM.md
skills/workflow-management-nextflow-pipelines/usage-guide.md
skills/workflow-management-nextflow-pipelines/examples/rnaseq.nf
skills/workflow-management-nextflow-pipelines/licenses/bioskills/LICENSE
skills/workflow-management-nf-core-pipelines/DNAKIT.md
skills/workflow-management-nf-core-pipelines/SKILL.md
skills/workflow-management-nf-core-pipelines/UPSTREAM.md
skills/workflow-management-nf-core-pipelines/usage-guide.md
skills/workflow-management-nf-core-pipelines/examples/run_nf_core.sh
skills/workflow-management-nf-core-pipelines/examples/samplesheet.csv
skills/workflow-management-nf-core-pipelines/licenses/bioskills/LICENSE
skills/workflow-management-snakemake-workflows/DNAKIT.md
skills/workflow-management-snakemake-workflows/SKILL.md
skills/workflow-management-snakemake-workflows/UPSTREAM.md
skills/workflow-management-snakemake-workflows/usage-guide.md
skills/workflow-management-snakemake-workflows/examples/rnaseq_snakefile
skills/workflow-management-snakemake-workflows/examples/scripts/run_deseq2.R
skills/workflow-management-snakemake-workflows/licenses/bioskills/LICENSE
skills/workflow-management-wdl-workflows/DNAKIT.md
skills/workflow-management-wdl-workflows/SKILL.md
skills/workflow-management-wdl-workflows/UPSTREAM.md
skills/workflow-management-wdl-workflows/usage-guide.md
skills/workflow-management-wdl-workflows/examples/rnaseq.wdl
skills/workflow-management-wdl-workflows/licenses/bioskills/LICENSE
skills/workflow-methods-docwriter/DNAKIT.md
skills/workflow-methods-docwriter/SKILL.md
skills/workflow-methods-docwriter/UPSTREAM.md
skills/workflow-methods-docwriter/requirements.txt
skills/workflow-methods-docwriter/examples/run_manifest.example.yaml
skills/workflow-methods-docwriter/fixtures/cwl/provenance.json
skills/workflow-methods-docwriter/fixtures/nextflow/outputs.txt
skills/workflow-methods-docwriter/fixtures/nextflow/tool-versions.json
skills/workflow-methods-docwriter/fixtures/nextflow/trace.txt
skills/workflow-methods-docwriter/fixtures/nextflow/work/ab/cdef/.command.in
skills/workflow-methods-docwriter/fixtures/nextflow/work/ab/cdef/.command.out
skills/workflow-methods-docwriter/fixtures/nextflow/work/ab/cdef/.command.sh
skills/workflow-methods-docwriter/fixtures/snakemake/jobs.jsonl
skills/workflow-methods-docwriter/fixtures/snakemake/outputs.txt
skills/workflow-methods-docwriter/licenses/omics/LICENSE
skills/workflow-methods-docwriter/reference/evidence-checklist.md
skills/workflow-methods-docwriter/reference/standards.md
skills/workflow-methods-docwriter/schemas/bio-paper-schema.yaml
skills/workflow-methods-docwriter/schemas/run-manifest.schema.json
skills/workflow-methods-docwriter/schemas/workflow-run-schema.yaml
skills/workflow-methods-docwriter/scripts/extract_cwl_run.py
skills/workflow-methods-docwriter/scripts/extract_nextflow_run.py
skills/workflow-methods-docwriter/scripts/extract_snakemake_run.py
skills/workflow-methods-docwriter/scripts/validate_run_manifest.py
skills/workflow-methods-docwriter/templates/methods_report.md
skills/workflow-methods-docwriter/templates/paper_summary.yaml
skills/workflows-atacseq-pipeline/DNAKIT.md
skills/workflows-atacseq-pipeline/SKILL.md
skills/workflows-atacseq-pipeline/UPSTREAM.md
skills/workflows-atacseq-pipeline/usage-guide.md
skills/workflows-atacseq-pipeline/examples/atacseq_workflow.sh
skills/workflows-atacseq-pipeline/examples/differential_atac.R
skills/workflows-atacseq-pipeline/licenses/bioskills/LICENSE
skills/workflows-causal-genomics-pipeline/DNAKIT.md
skills/workflows-causal-genomics-pipeline/SKILL.md
skills/workflows-causal-genomics-pipeline/UPSTREAM.md
skills/workflows-causal-genomics-pipeline/usage-guide.md
skills/workflows-causal-genomics-pipeline/examples/post_gwas_causal_pipeline.R
skills/workflows-causal-genomics-pipeline/licenses/bioskills/LICENSE
skills/workflows-chipseq-pipeline/DNAKIT.md
skills/workflows-chipseq-pipeline/SKILL.md
skills/workflows-chipseq-pipeline/UPSTREAM.md
skills/workflows-chipseq-pipeline/usage-guide.md
skills/workflows-chipseq-pipeline/examples/narrow_peak_workflow.sh
skills/workflows-chipseq-pipeline/examples/peak_annotation.R
skills/workflows-chipseq-pipeline/licenses/bioskills/LICENSE
skills/workflows-cnv-pipeline/DNAKIT.md
skills/workflows-cnv-pipeline/SKILL.md
skills/workflows-cnv-pipeline/UPSTREAM.md
skills/workflows-cnv-pipeline/usage-guide.md
skills/workflows-cnv-pipeline/examples/cnvkit_workflow.sh
skills/workflows-cnv-pipeline/licenses/bioskills/LICENSE
skills/workflows-crispr-editing-pipeline/DNAKIT.md
skills/workflows-crispr-editing-pipeline/SKILL.md
skills/workflows-crispr-editing-pipeline/UPSTREAM.md
skills/workflows-crispr-editing-pipeline/usage-guide.md
skills/workflows-crispr-editing-pipeline/examples/crispr_editing_workflow.py
skills/workflows-crispr-editing-pipeline/licenses/bioskills/LICENSE
skills/workflows-crispr-screen-pipeline/DNAKIT.md
skills/workflows-crispr-screen-pipeline/SKILL.md
skills/workflows-crispr-screen-pipeline/UPSTREAM.md
skills/workflows-crispr-screen-pipeline/usage-guide.md
skills/workflows-crispr-screen-pipeline/examples/crispr_pipeline.sh
skills/workflows-crispr-screen-pipeline/licenses/bioskills/LICENSE
skills/workflows-edna-pipeline/DNAKIT.md
skills/workflows-edna-pipeline/SKILL.md
skills/workflows-edna-pipeline/UPSTREAM.md
skills/workflows-edna-pipeline/usage-guide.md
skills/workflows-edna-pipeline/examples/edna_pipeline.R
skills/workflows-edna-pipeline/examples/edna_pipeline.sh
skills/workflows-edna-pipeline/licenses/bioskills/LICENSE
skills/workflows-fastq-to-variants/DNAKIT.md
skills/workflows-fastq-to-variants/SKILL.md
skills/workflows-fastq-to-variants/UPSTREAM.md
skills/workflows-fastq-to-variants/usage-guide.md
skills/workflows-fastq-to-variants/examples/bwa_bcftools_workflow.sh
skills/workflows-fastq-to-variants/examples/bwa_gatk_workflow.sh
skills/workflows-fastq-to-variants/licenses/bioskills/LICENSE
skills/workflows-genome-annotation-pipeline/DNAKIT.md
skills/workflows-genome-annotation-pipeline/SKILL.md
skills/workflows-genome-annotation-pipeline/UPSTREAM.md
skills/workflows-genome-annotation-pipeline/usage-guide.md
skills/workflows-genome-annotation-pipeline/examples/eukaryotic_annotation_pipeline.sh
skills/workflows-genome-annotation-pipeline/examples/prokaryotic_annotation_pipeline.sh
skills/workflows-genome-annotation-pipeline/licenses/bioskills/LICENSE
skills/workflows-genome-assembly-pipeline/DNAKIT.md
skills/workflows-genome-assembly-pipeline/SKILL.md
skills/workflows-genome-assembly-pipeline/UPSTREAM.md
skills/workflows-genome-assembly-pipeline/usage-guide.md
skills/workflows-genome-assembly-pipeline/examples/bacterial_assembly.sh
skills/workflows-genome-assembly-pipeline/licenses/bioskills/LICENSE
skills/workflows-gwas-pipeline/DNAKIT.md
skills/workflows-gwas-pipeline/SKILL.md
skills/workflows-gwas-pipeline/UPSTREAM.md
skills/workflows-gwas-pipeline/usage-guide.md
skills/workflows-gwas-pipeline/examples/gwas_workflow.sh
skills/workflows-gwas-pipeline/licenses/bioskills/LICENSE
skills/workflows-hic-pipeline/DNAKIT.md
skills/workflows-hic-pipeline/SKILL.md
skills/workflows-hic-pipeline/UPSTREAM.md
skills/workflows-hic-pipeline/usage-guide.md
skills/workflows-hic-pipeline/examples/hic_analysis.py
skills/workflows-hic-pipeline/licenses/bioskills/LICENSE
skills/workflows-liquid-biopsy-pipeline/DNAKIT.md
skills/workflows-liquid-biopsy-pipeline/SKILL.md
skills/workflows-liquid-biopsy-pipeline/UPSTREAM.md
skills/workflows-liquid-biopsy-pipeline/usage-guide.md
skills/workflows-liquid-biopsy-pipeline/examples/liquid_biopsy_pipeline.py
skills/workflows-liquid-biopsy-pipeline/licenses/bioskills/LICENSE
skills/workflows-longread-sv-pipeline/DNAKIT.md
skills/workflows-longread-sv-pipeline/SKILL.md
skills/workflows-longread-sv-pipeline/UPSTREAM.md
skills/workflows-longread-sv-pipeline/usage-guide.md
skills/workflows-longread-sv-pipeline/examples/ont_sv_calling.sh
skills/workflows-longread-sv-pipeline/licenses/bioskills/LICENSE
skills/workflows-metagenomics-pipeline/DNAKIT.md
skills/workflows-metagenomics-pipeline/SKILL.md
skills/workflows-metagenomics-pipeline/UPSTREAM.md
skills/workflows-metagenomics-pipeline/usage-guide.md
skills/workflows-metagenomics-pipeline/examples/metagenomics_workflow.sh
skills/workflows-metagenomics-pipeline/licenses/bioskills/LICENSE
skills/workflows-methylation-pipeline/DNAKIT.md
skills/workflows-methylation-pipeline/SKILL.md
skills/workflows-methylation-pipeline/UPSTREAM.md
skills/workflows-methylation-pipeline/usage-guide.md
skills/workflows-methylation-pipeline/examples/methylkit_analysis.R
skills/workflows-methylation-pipeline/licenses/bioskills/LICENSE
skills/workflows-microbiome-pipeline/DNAKIT.md
skills/workflows-microbiome-pipeline/SKILL.md
skills/workflows-microbiome-pipeline/UPSTREAM.md
skills/workflows-microbiome-pipeline/usage-guide.md
skills/workflows-microbiome-pipeline/examples/microbiome_workflow.R
skills/workflows-microbiome-pipeline/licenses/bioskills/LICENSE
skills/workflows-multiome-pipeline/DNAKIT.md
skills/workflows-multiome-pipeline/SKILL.md
skills/workflows-multiome-pipeline/UPSTREAM.md
skills/workflows-multiome-pipeline/usage-guide.md
skills/workflows-multiome-pipeline/examples/multiome_workflow.R
skills/workflows-multiome-pipeline/licenses/bioskills/LICENSE
skills/workflows-neoantigen-pipeline/DNAKIT.md
skills/workflows-neoantigen-pipeline/SKILL.md
skills/workflows-neoantigen-pipeline/UPSTREAM.md
skills/workflows-neoantigen-pipeline/usage-guide.md
skills/workflows-neoantigen-pipeline/examples/neoantigen_workflow.py
skills/workflows-neoantigen-pipeline/licenses/bioskills/LICENSE
skills/workflows-outbreak-pipeline/DNAKIT.md
skills/workflows-outbreak-pipeline/SKILL.md
skills/workflows-outbreak-pipeline/UPSTREAM.md
skills/workflows-outbreak-pipeline/usage-guide.md
skills/workflows-outbreak-pipeline/examples/outbreak_workflow.sh
skills/workflows-outbreak-pipeline/licenses/bioskills/LICENSE
skills/workflows-somatic-variant-pipeline/DNAKIT.md
skills/workflows-somatic-variant-pipeline/SKILL.md
skills/workflows-somatic-variant-pipeline/UPSTREAM.md
skills/workflows-somatic-variant-pipeline/usage-guide.md
skills/workflows-somatic-variant-pipeline/examples/run_mutect2.sh
skills/workflows-somatic-variant-pipeline/licenses/bioskills/LICENSE
skills/workflows-tcr-pipeline/DNAKIT.md
skills/workflows-tcr-pipeline/SKILL.md
skills/workflows-tcr-pipeline/UPSTREAM.md
skills/workflows-tcr-pipeline/usage-guide.md
skills/workflows-tcr-pipeline/examples/tcr_full_pipeline.sh
skills/workflows-tcr-pipeline/licenses/bioskills/LICENSE
skills/write-sequences/DNAKIT.md
skills/write-sequences/SKILL.md
skills/write-sequences/UPSTREAM.md
skills/write-sequences/usage-guide.md
skills/write-sequences/examples/basic_writing.py
skills/write-sequences/licenses/bioskills/LICENSE
src/dnakit/__init__.py
src/dnakit/_backend_errors.py
src/dnakit/_checkpoint_status.py
src/dnakit/_dependency_hints.py
src/dnakit/_download_progress.py
src/dnakit/_io_progress.py
src/dnakit/_network_retry.py
src/dnakit/_parallel.py
src/dnakit/_progress.py
src/dnakit/_verbosity.py
src/dnakit/_version.py
src/dnakit/batch.py
src/dnakit/chunking.py
src/dnakit/exceptions.py
src/dnakit/py.typed
src/dnakit.egg-info/PKG-INFO
src/dnakit.egg-info/SOURCES.txt
src/dnakit.egg-info/dependency_links.txt
src/dnakit.egg-info/entry_points.txt
src/dnakit.egg-info/requires.txt
src/dnakit.egg-info/top_level.txt
src/dnakit/_processing/__init__.py
src/dnakit/_processing/datasets.py
src/dnakit/_processing/dispatch.py
src/dnakit/_processing/file_split.py
src/dnakit/_processing/fragments.py
src/dnakit/_processing/indexed_records.py
src/dnakit/_processing/inputs.py
src/dnakit/_processing/multiple.py
src/dnakit/_processing/positioned_split.py
src/dnakit/_processing/progress.py
src/dnakit/_processing/regions.py
src/dnakit/_processing/sequence.py
src/dnakit/_processing/split_exports.py
src/dnakit/alignment/__init__.py
src/dnakit/alignment/pairwise.py
src/dnakit/alignment/results.py
src/dnakit/annotation/__init__.py
src/dnakit/annotation/_gene_mapping.py
src/dnakit/annotation/_gene_reference.py
src/dnakit/annotation/gene_models.py
src/dnakit/annotation/genes.py
src/dnakit/annotation/variants.py
src/dnakit/backends/__init__.py
src/dnakit/backends/external.py
src/dnakit/backends/registry.py
src/dnakit/backends/scientific.py
src/dnakit/bioinformatics/__init__.py
src/dnakit/bioinformatics/_common.py
src/dnakit/bioinformatics/alignment.py
src/dnakit/bioinformatics/cloning.py
src/dnakit/bioinformatics/counts.py
src/dnakit/bioinformatics/encoding.py
src/dnakit/bioinformatics/features.py
src/dnakit/bioinformatics/metrics.py
src/dnakit/bioinformatics/motifs.py
src/dnakit/bioinformatics/ngs.py
src/dnakit/bioinformatics/optimization.py
src/dnakit/bioinformatics/phylogeny.py
src/dnakit/bioinformatics/reads.py
src/dnakit/bioinformatics/statistics.py
src/dnakit/bioinformatics/workflows.py
src/dnakit/cache/__init__.py
src/dnakit/cache/store.py
src/dnakit/cli/__init__.py
src/dnakit/cli/__main__.py
src/dnakit/cli/app.py
src/dnakit/cli/database.py
src/dnakit/cli/gene_annotation.py
src/dnakit/cli/skills.py
src/dnakit/cli/visualization.py
src/dnakit/cli/workflow.py
src/dnakit/comparative/__init__.py
src/dnakit/comparative/selection.py
src/dnakit/config/__init__.py
src/dnakit/config/loader.py
src/dnakit/core/__init__.py
src/dnakit/core/_json.py
src/dnakit/core/backend_info.py
src/dnakit/core/collection.py
src/dnakit/core/coordinates.py
src/dnakit/core/enums.py
src/dnakit/core/facade.py
src/dnakit/core/feature.py
src/dnakit/core/gap.py
src/dnakit/core/issues.py
src/dnakit/core/provenance.py
src/dnakit/core/record.py
src/dnakit/core/results.py
src/dnakit/core/sequence.py
src/dnakit/databases/__init__.py
src/dnakit/databases/_extensions.py
src/dnakit/databases/_generated.py
src/dnakit/databases/_regulatory.py
src/dnakit/databases/_routes.py
src/dnakit/databases/_runtime.py
src/dnakit/databases/providers.json
src/dnakit/databases/_providers/LICENSE
src/dnakit/databases/_providers/UPSTREAM.json
src/dnakit/databases/_providers/__init__.py
src/dnakit/databases/_providers/alliance_genome_tool.py
src/dnakit/databases/_providers/alphafold_tool.py
src/dnakit/databases/_providers/alphagenome_tool.py
src/dnakit/databases/_providers/alphamissense_tool.py
src/dnakit/databases/_providers/arxiv_tool.py
src/dnakit/databases/_providers/base_rest_tool.py
src/dnakit/databases/_providers/base_tool.py
src/dnakit/databases/_providers/biogrid_tool.py
src/dnakit/databases/_providers/biorxiv_tool.py
src/dnakit/databases/_providers/blast_tool.py
src/dnakit/databases/_providers/bvbrc_tool.py
src/dnakit/databases/_providers/cadd_tool.py
src/dnakit/databases/_providers/cbioportal_tool.py
src/dnakit/databases/_providers/cellxgene_census_tool.py
src/dnakit/databases/_providers/chem_tool.py
src/dnakit/databases/_providers/chipatlas_tool.py
src/dnakit/databases/_providers/civic_tool.py
src/dnakit/databases/_providers/clingen_dosage_tool.py
src/dnakit/databases/_providers/clingen_tool.py
src/dnakit/databases/_providers/clinvar_tool.py
src/dnakit/databases/_providers/cosmic_tool.py
src/dnakit/databases/_providers/crossref_tool.py
src/dnakit/databases/_providers/ctd_tool.py
src/dnakit/databases/_providers/ctg_tool.py
src/dnakit/databases/_providers/dataset_tool.py
src/dnakit/databases/_providers/dbsnp_tool.py
src/dnakit/databases/_providers/depmap_tool.py
src/dnakit/databases/_providers/dgidb_tool.py
src/dnakit/databases/_providers/disgenet_tool.py
src/dnakit/databases/_providers/dn_ds_tool.py
src/dnakit/databases/_providers/dna_tools.py
src/dnakit/databases/_providers/dynamut2_tool.py
src/dnakit/databases/_providers/efo_tool.py
src/dnakit/databases/_providers/ena_portal_tool.py
src/dnakit/databases/_providers/encode_tool.py
src/dnakit/databases/_providers/enrichr_ext_tool.py
src/dnakit/databases/_providers/enrichr_tool.py
src/dnakit/databases/_providers/ensembl_compara_tool.py
src/dnakit/databases/_providers/ensembl_sequence_tool.py
src/dnakit/databases/_providers/ensembl_tool.py
src/dnakit/databases/_providers/ensembl_variation_ext_tool.py
src/dnakit/databases/_providers/ensembl_vep_tool.py
src/dnakit/databases/_providers/epigenomics_tool.py
src/dnakit/databases/_providers/esm2_variant_effect_tool.py
src/dnakit/databases/_providers/esm_tool.py
src/dnakit/databases/_providers/europe_pmc_tool.py
src/dnakit/databases/_providers/eve_tool.py
src/dnakit/databases/_providers/evo2_variant_effect_tool.py
src/dnakit/databases/_providers/exceptions.py
src/dnakit/databases/_providers/executed_notebook_tool.py
src/dnakit/databases/_providers/expression_atlas_tool.py
src/dnakit/databases/_providers/favor_tool.py
src/dnakit/databases/_providers/file_download_tool.py
src/dnakit/databases/_providers/finngen_tool.py
src/dnakit/databases/_providers/fourdn_tool.py
src/dnakit/databases/_providers/gbif_tool.py
src/dnakit/databases/_providers/gdc_tool.py
src/dnakit/databases/_providers/gencc_tool.py
src/dnakit/databases/_providers/gene_ontology_tool.py
src/dnakit/databases/_providers/genomics_gene_search_tool.py
src/dnakit/databases/_providers/gnomad_tool.py
src/dnakit/databases/_providers/graphql_tool.py
src/dnakit/databases/_providers/gtdb_tool.py
src/dnakit/databases/_providers/gtex_tool.py
src/dnakit/databases/_providers/gtex_v2_tool.py
src/dnakit/databases/_providers/gwas_tool.py
src/dnakit/databases/_providers/harmonizome_tool.py
src/dnakit/databases/_providers/hgnc_tool.py
src/dnakit/databases/_providers/hpa_tool.py
src/dnakit/databases/_providers/hpo_tool.py
src/dnakit/databases/_providers/http_utils.py
src/dnakit/databases/_providers/huggingface_inference_tool.py
src/dnakit/databases/_providers/humanbase_tool.py
src/dnakit/databases/_providers/iedb_tool.py
src/dnakit/databases/_providers/igsr_tool.py
src/dnakit/databases/_providers/imgt_tool.py
src/dnakit/databases/_providers/immport_tool.py
src/dnakit/databases/_providers/intact_tool.py
src/dnakit/databases/_providers/interpro_entry_tool.py
src/dnakit/databases/_providers/interpro_tool.py
src/dnakit/databases/_providers/jaspar_tool.py
src/dnakit/databases/_providers/kegg_ext_tool.py
src/dnakit/databases/_providers/kegg_tool.py
src/dnakit/databases/_providers/ldlink_tool.py
src/dnakit/databases/_providers/logging_config.py
src/dnakit/databases/_providers/marrvel_tool.py
src/dnakit/databases/_providers/mavedb_tool.py
src/dnakit/databases/_providers/mcp_client_tool.py
src/dnakit/databases/_providers/metabolite_tool.py
src/dnakit/databases/_providers/mgnify_expanded_tool.py
src/dnakit/databases/_providers/mgnify_tool.py
src/dnakit/databases/_providers/monarch_v3_tool.py
src/dnakit/databases/_providers/mygene_tool.py
src/dnakit/databases/_providers/ncbi_datasets_tool.py
src/dnakit/databases/_providers/ncbi_eutils_tool.py
src/dnakit/databases/_providers/ncbi_nucleotide_tool.py
src/dnakit/databases/_providers/ncbi_sra_tool.py
src/dnakit/databases/_providers/nvidia_nim_tool.py
src/dnakit/databases/_providers/ols_tool.py
src/dnakit/databases/_providers/omim_tool.py
src/dnakit/databases/_providers/oncokb_tool.py
src/dnakit/databases/_providers/openalex_tool.py
src/dnakit/databases/_providers/openfda_adv_tool.py
src/dnakit/databases/_providers/openfda_tool.py
src/dnakit/databases/_providers/orphanet_tool.py
src/dnakit/databases/_providers/panther_tool.py
src/dnakit/databases/_providers/pdbe_sifts_tool.py
src/dnakit/databases/_providers/pfam_tool.py
src/dnakit/databases/_providers/pheweb_phewas_tool.py
src/dnakit/databases/_providers/plant_reactome_tool.py
src/dnakit/databases/_providers/progenetix_tool.py
src/dnakit/databases/_providers/proteins_api_tool.py
src/dnakit/databases/_providers/pubchem_tool.py
src/dnakit/databases/_providers/pubmed_tool.py
src/dnakit/databases/_providers/quickgo_tool.py
src/dnakit/databases/_providers/rcsb_data_tool.py
src/dnakit/databases/_providers/reactome_analysis_tool.py
src/dnakit/databases/_providers/reactome_content_tool.py
src/dnakit/databases/_providers/reactome_tool.py
src/dnakit/databases/_providers/regulomedb_tool.py
src/dnakit/databases/_providers/remap_tool.py
src/dnakit/databases/_providers/restful_tool.py
src/dnakit/databases/_providers/rgd_strain_tool.py
src/dnakit/databases/_providers/rgd_tool.py
src/dnakit/databases/_providers/scientific_calculator_tools.py
src/dnakit/databases/_providers/screen_tool.py
src/dnakit/databases/_providers/semantic_scholar_tool.py
src/dnakit/databases/_providers/sequence_analyze_tool.py
src/dnakit/databases/_providers/sgd_tool.py
src/dnakit/databases/_providers/spliceai_tool.py
src/dnakit/databases/_providers/sra_tool.py
src/dnakit/databases/_providers/string_ext_tool.py
src/dnakit/databases/_providers/string_tool.py
src/dnakit/databases/_providers/structure_annotation_tool.py
src/dnakit/databases/_providers/tark_tool.py
src/dnakit/databases/_providers/tool_discovery_tools.py
src/dnakit/databases/_providers/tool_registry.py
src/dnakit/databases/_providers/unibind_tool.py
src/dnakit/databases/_providers/uniprot_tool.py
src/dnakit/databases/_providers/usda_plants_tool.py
src/dnakit/databases/_providers/utils.py
src/dnakit/databases/_providers/variant_fraction_tool.py
src/dnakit/databases/_providers/vcf_stats_tool.py
src/dnakit/databases/_providers/web_search_tool.py
src/dnakit/databases/_providers/wikipathways_tool.py
src/dnakit/databases/_providers/wormbase_tool.py
src/dnakit/databases/_providers/xenbase_tool.py
src/dnakit/databases/_providers/xml_tool.py
src/dnakit/databases/_providers/cache/__init__.py
src/dnakit/databases/_providers/cache/memory_cache.py
src/dnakit/databases/_providers/data/__init__.py
src/dnakit/databases/_providers/data/fda_drugs_with_brand_generic_names_for_tool.py
src/dnakit/databases/_providers/data/mcpautoloadertool_defaults.json
src/dnakit/databases/_providers/data/toolfinderkeyword_defaults.json
src/dnakit/datasets/__init__.py
src/dnakit/datasets/_advanced_shared.py
src/dnakit/datasets/_metadata.py
src/dnakit/datasets/advanced_deduplicate.py
src/dnakit/datasets/advanced_split.py
src/dnakit/datasets/clustering.py
src/dnakit/datasets/config.py
src/dnakit/datasets/deduplicate.py
src/dnakit/datasets/evaluation.py
src/dnakit/datasets/file_results.py
src/dnakit/datasets/filter.py
src/dnakit/datasets/neural_clustering.py
src/dnakit/datasets/results.py
src/dnakit/datasets/sampling.py
src/dnakit/datasets/split.py
src/dnakit/datasets/tabular.py
src/dnakit/descriptors/__init__.py
src/dnakit/descriptors/_dinucleotide.py
src/dnakit/descriptors/_shared.py
src/dnakit/descriptors/all.py
src/dnakit/descriptors/basic.py
src/dnakit/descriptors/codon.py
src/dnakit/descriptors/complexity.py
src/dnakit/descriptors/entropy.py
src/dnakit/descriptors/homopolymer.py
src/dnakit/descriptors/kmer.py
src/dnakit/descriptors/results.py
src/dnakit/descriptors/schema.py
src/dnakit/descriptors/window.py
src/dnakit/download/__init__.py
src/dnakit/download/_sequence.py
src/dnakit/download/catalogs.py
src/dnakit/download/ena.py
src/dnakit/download/encode.py
src/dnakit/download/files.py
src/dnakit/download/indexes.py
src/dnakit/download/metadata.py
src/dnakit/download/models.py
src/dnakit/download/ncbi.py
src/dnakit/download/sequence.py
src/dnakit/download/ucsc.py
src/dnakit/encode/__init__.py
src/dnakit/encode/_runtime.py
src/dnakit/encode/_backend/LICENSE
src/dnakit/encode/_backend/UPSTREAM.json
src/dnakit/encode/_backend/__init__.py
src/dnakit/encode/_backend/client/__init__.py
src/dnakit/encode/_backend/client/auth.py
src/dnakit/encode/_backend/client/constants.py
src/dnakit/encode/_backend/client/downloader.py
src/dnakit/encode/_backend/client/encode_client.py
src/dnakit/encode/_backend/client/models.py
src/dnakit/encode/_backend/client/tracker.py
src/dnakit/encode/_backend/client/validation.py
src/dnakit/encode/_backend/server/__init__.py
src/dnakit/encode/_backend/server/main.py
src/dnakit/evaluation/__init__.py
src/dnakit/evaluation/_frechet_plots.py
src/dnakit/evaluation/_plots.py
src/dnakit/evaluation/_shared.py
src/dnakit/evaluation/collection.py
src/dnakit/evaluation/config.py
src/dnakit/evaluation/distribution.py
src/dnakit/evaluation/frechet.py
src/dnakit/evaluation/generative.py
src/dnakit/evaluation/reference.py
src/dnakit/evaluation/reference_consistency.py
src/dnakit/evaluation/results.py
src/dnakit/evaluation/scorecard.py
src/dnakit/evaluation/sequence.py
src/dnakit/evaluation/synthesis.py
src/dnakit/fingerprints/__init__.py
src/dnakit/fingerprints/_shared.py
src/dnakit/fingerprints/advanced.py
src/dnakit/fingerprints/bit.py
src/dnakit/fingerprints/encoding.py
src/dnakit/fingerprints/kmer.py
src/dnakit/fingerprints/results.py
src/dnakit/fingerprints/sketch.py
src/dnakit/generated/__init__.py
src/dnakit/generated/manifest.json
src/dnakit/genomics/__init__.py
src/dnakit/genomics/ani.py
src/dnakit/genomics/breeding.py
src/dnakit/genomics/genes.py
src/dnakit/genomics/methylation.py
src/dnakit/genomics/nanotechnology.py
src/dnakit/genomics/population.py
src/dnakit/genomics/storage.py
src/dnakit/integrations/__init__.py
src/dnakit/integrations/analyses.json
src/dnakit/integrations/catalog.py
src/dnakit/integrations/execution.py
src/dnakit/integrations/mcp.py
src/dnakit/integrations/mcp_servers.json
src/dnakit/integrations/projects.json
src/dnakit/io/__init__.py
src/dnakit/io/_advanced_common.py
src/dnakit/io/_formats.py
src/dnakit/io/annotations.py
src/dnakit/io/api.py
src/dnakit/io/artifacts.py
src/dnakit/io/config.py
src/dnakit/io/genbank.py
src/dnakit/io/indexed.py
src/dnakit/io/inputs.py
src/dnakit/io/metadata.py
src/dnakit/io/parquet.py
src/dnakit/io/results.py
src/dnakit/io/rows.py
src/dnakit/io/source.py
src/dnakit/io/tables.py
src/dnakit/llm/__init__.py
src/dnakit/llm/client.py
src/dnakit/llm/files.py
src/dnakit/llm/models.py
src/dnakit/llm/providers.py
src/dnakit/molbio/__init__.py
src/dnakit/molbio/_shared.py
src/dnakit/molbio/assembly.py
src/dnakit/molbio/crispr.py
src/dnakit/molbio/golden_gate.py
src/dnakit/molbio/optimization.py
src/dnakit/molbio/primer3_design.py
src/dnakit/molbio/primers.py
src/dnakit/molbio/restriction.py
src/dnakit/molbio/results.py
src/dnakit/ops/__init__.py
src/dnakit/ops/_common.py
src/dnakit/ops/_fasta_direction.py
src/dnakit/ops/_file_direction.py
src/dnakit/ops/circular.py
src/dnakit/ops/concat.py
src/dnakit/ops/direction.py
src/dnakit/ops/edit.py
src/dnakit/ops/evolution.py
src/dnakit/ops/mutation.py
src/dnakit/ops/records.py
src/dnakit/ops/translation.py
src/dnakit/patterns/__init__.py
src/dnakit/patterns/_shared.py
src/dnakit/patterns/coding.py
src/dnakit/patterns/crispr.py
src/dnakit/patterns/motif.py
src/dnakit/patterns/regions.py
src/dnakit/patterns/repeats.py
src/dnakit/patterns/restriction.py
src/dnakit/patterns/results.py
src/dnakit/predictions/__init__.py
src/dnakit/predictions/api.py
src/dnakit/predictions/backends.py
src/dnakit/predictions/checkpoints.py
src/dnakit/predictions/enformer_benchmarks.py
src/dnakit/predictions/models.py
src/dnakit/predictions/results.py
src/dnakit/predictions/custom_training/__init__.py
src/dnakit/predictions/custom_training/_loading.py
src/dnakit/predictions/custom_training/data.py
src/dnakit/predictions/custom_training/encoder.py
src/dnakit/predictions/custom_training/encoder_alphagenome.py
src/dnakit/predictions/custom_training/encoder_enformer.py
src/dnakit/predictions/custom_training/encoder_factory.py
src/dnakit/predictions/custom_training/encoder_native.py
src/dnakit/predictions/custom_training/llm.py
src/dnakit/predictions/custom_training/ml_features.py
src/dnakit/predictions/custom_training/ml_models.py
src/dnakit/predictions/custom_training/ml_training.py
src/dnakit/predictions/custom_training/providers.py
src/dnakit/predictions/custom_training/schema.py
src/dnakit/predictions/custom_training/splitting.py
src/dnakit/predictions/custom_training/targets.py
src/dnakit/predictions/custom_training/training.py
src/dnakit/references/__init__.py
src/dnakit/references/models.py
src/dnakit/references/ncbi.py
src/dnakit/representations/__init__.py
src/dnakit/representations/backends.py
src/dnakit/representations/checkpoints.py
src/dnakit/representations/extraction.py
src/dnakit/representations/models.py
src/dnakit/representations/results.py
src/dnakit/search/__init__.py
src/dnakit/search/_http.py
src/dnakit/search/_shared.py
src/dnakit/search/blast.py
src/dnakit/search/ena.py
src/dnakit/search/encode.py
src/dnakit/search/ensembl.py
src/dnakit/search/models.py
src/dnakit/search/ncbi.py
src/dnakit/search/ucsc.py
src/dnakit/search/web.py
src/dnakit/secondary_structure/__init__.py
src/dnakit/secondary_structure/dotbracket.py
src/dnakit/secondary_structure/nupack.py
src/dnakit/secondary_structure/results.py
src/dnakit/similarity/__init__.py
src/dnakit/similarity/_shared.py
src/dnakit/similarity/approximate.py
src/dnakit/similarity/compare.py
src/dnakit/similarity/dashing.py
src/dnakit/similarity/distance.py
src/dnakit/similarity/index.py
src/dnakit/similarity/matrix.py
src/dnakit/similarity/results.py
src/dnakit/similarity/search.py
src/dnakit/similarity/sketch.py
src/dnakit/similarity/vector.py
src/dnakit/skills/__init__.py
src/dnakit/skills/catalog.py
src/dnakit/skills/install.py
src/dnakit/standardize/__init__.py
src/dnakit/standardize/_shared.py
src/dnakit/standardize/config.py
src/dnakit/standardize/gaps.py
src/dnakit/standardize/normalize.py
src/dnakit/standardize/results.py
src/dnakit/standardize/validate.py
src/dnakit/structure3d/__init__.py
src/dnakit/structure3d/_shared.py
src/dnakit/structure3d/geometry.py
src/dnakit/structure3d/pdb.py
src/dnakit/structure3d/results.py
src/dnakit/structure3d/threedna.py
src/dnakit/thermodynamics/__init__.py
src/dnakit/thermodynamics/_shared.py
src/dnakit/thermodynamics/backends.py
src/dnakit/thermodynamics/calculations.py
src/dnakit/thermodynamics/config.py
src/dnakit/thermodynamics/equilibrium.py
src/dnakit/thermodynamics/optics.py
src/dnakit/thermodynamics/parameters.py
src/dnakit/thermodynamics/results.py
src/dnakit/tools/__init__.py
src/dnakit/tools/adapters.py
src/dnakit/tools/agent.py
src/dnakit/tools/catalog.py
src/dnakit/tools/checkpoint.py
src/dnakit/tools/compatibility.py
src/dnakit/tools/contributions.py
src/dnakit/tools/descriptions.py
src/dnakit/tools/development_quality.py
src/dnakit/tools/development_support.py
src/dnakit/tools/embeddings.py
src/dnakit/tools/execution.py
src/dnakit/tools/generation.py
src/dnakit/tools/knowledge.py
src/dnakit/tools/optimization.py
src/dnakit/tools/registry.py
src/dnakit/tools/repair.py
src/dnakit/tools/runtime_updates.py
src/dnakit/tools/serialization.py
src/dnakit/tools/server.py
src/dnakit/tools/_data/descriptions.json
src/dnakit/visualization/__init__.py
src/dnakit/visualization/_svg.py
src/dnakit/visualization/advanced.py
src/dnakit/visualization/config.py
src/dnakit/visualization/confusion.py
src/dnakit/visualization/distribution.py
src/dnakit/visualization/embedding_errors.py
src/dnakit/visualization/export.py
src/dnakit/visualization/figure.py
src/dnakit/visualization/learning.py
src/dnakit/visualization/matrix.py
src/dnakit/visualization/metric.py
src/dnakit/visualization/report.py
src/dnakit/visualization/results.py
src/dnakit/visualization/sequence.py
src/dnakit/workflows/__init__.py
src/dnakit/workflows/execution.py
src/dnakit/workflows/inheritance.py
src/dnakit/workflows/manifest.py
src/dnakit/workflows/reporting.py
src/dnakit/workflows/runner.py
src/dnakit/workflows/schema.py
src/dnakit/workflows/common/LICENSE
src/dnakit/workflows/common/UPSTREAM.json
src/dnakit/workflows/common/__init__.py
src/dnakit/workflows/common/audit.py
src/dnakit/workflows/common/checksums.py
src/dnakit/workflows/common/html_report.py
src/dnakit/workflows/common/parsers.py
src/dnakit/workflows/common/portable_commands.py
src/dnakit/workflows/common/profile.py
src/dnakit/workflows/common/rec_shortener.py
src/dnakit/workflows/common/report.py
src/dnakit/workflows/common/reproducibility.py
src/dnakit/workflows/common/sarek.py
src/dnakit/workflows/common/scrna_io.py
src/dnakit/workflows/common/textio.py
src/dnakit/workflows/common/vcf_qc.py
src/dnakit/workflows/prs/INTENTS.json
src/dnakit/workflows/prs/LICENSE
src/dnakit/workflows/prs/UPSTREAM.json
src/dnakit/workflows/prs/__init__.py
src/dnakit/workflows/prs/api.py
src/dnakit/workflows/prs/curated_scores.json
src/dnakit/workflows/prs/demo_patient_prs.txt
src/dnakit/workflows/prs/generate_curated_scores.py
src/dnakit/workflows/prs/gwas_prs.py
src/dnakit/workflows/prs/repro_bundle.py
src/dnakit/workflows/prs/data/CLAWBIO-AF-12_GRCh37.txt
src/dnakit/workflows/prs/data/CLAWBIO-BC-77_GRCh37.txt
src/dnakit/workflows/prs/data/CLAWBIO-BMI-97_GRCh37.txt
src/dnakit/workflows/prs/data/CLAWBIO-CAD-46_GRCh37.txt
src/dnakit/workflows/prs/data/CLAWBIO-PC-147_GRCh37.txt
src/dnakit/workflows/prs/data/CLAWBIO-T2D-8_GRCh37.txt
src/dnakit/workflows/support/LICENSE
src/dnakit/workflows/support/UPSTREAM.json
src/dnakit/workflows/support/__init__.py
src/dnakit/workflows/support/recombinator.py
src/dnakit/workflows/support/clinical_trial_finder/SKILL.md
src/dnakit/workflows/support/clinical_trial_finder/__init__.py
src/dnakit/workflows/support/clinical_trial_finder/api.py
src/dnakit/workflows/support/clinical_trial_finder/clinical_trial_finder.py
src/dnakit/workflows/support/clinical_trial_finder/constants.py
src/dnakit/workflows/support/clinical_trial_finder/demo_input.txt
src/dnakit/workflows/support/clinical_trial_finder/euctr.py
src/dnakit/workflows/support/clinical_trial_finder/gwas_bridge.py
src/dnakit/workflows/support/clinical_trial_finder/opentargets.py
src/dnakit/workflows/support/clinical_trial_finder/writers.py
src/dnakit/workflows/support/clinical_trial_finder/examples/README.md
src/dnakit/workflows/support/clinical_trial_finder/examples/demo_output/fhir_bundle.json
src/dnakit/workflows/support/clinical_trial_finder/examples/demo_output/report.md
src/dnakit/workflows/support/clinical_trial_finder/examples/demo_output/summary.json
src/dnakit/workflows/support/clinical_trial_finder/examples/demo_output/tables/trials.csv
src/dnakit/workflows/support/clinical_variant_reporter/SKILL.md
src/dnakit/workflows/support/clinical_variant_reporter/__init__.py
src/dnakit/workflows/support/clinical_variant_reporter/acmg_engine.py
src/dnakit/workflows/support/clinical_variant_reporter/clinical_variant_reporter.py
src/dnakit/workflows/support/clinical_variant_reporter/self_audit.py
src/dnakit/workflows/support/clinical_variant_reporter/example_data/demo_evidence_cache.json
src/dnakit/workflows/support/clinical_variant_reporter/example_data/giab_acmg_panel.vcf
src/dnakit/workflows/support/fine_mapping/SKILL.md
src/dnakit/workflows/support/fine_mapping/__init__.py
src/dnakit/workflows/support/fine_mapping/fine_mapping.py
src/dnakit/workflows/support/fine_mapping/fine_mapping_core/__init__.py
src/dnakit/workflows/support/fine_mapping/fine_mapping_core/abf.py
src/dnakit/workflows/support/fine_mapping/fine_mapping_core/credible_sets.py
src/dnakit/workflows/support/fine_mapping/fine_mapping_core/io.py
src/dnakit/workflows/support/fine_mapping/fine_mapping_core/report.py
src/dnakit/workflows/support/fine_mapping/fine_mapping_core/susie.py
src/dnakit/workflows/support/fine_mapping/fine_mapping_core/susie_inf.py
src/dnakit/workflows/support/gwas_lookup/INTENTS.json
src/dnakit/workflows/support/gwas_lookup/SKILL.md
src/dnakit/workflows/support/gwas_lookup/__init__.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup.py
src/dnakit/workflows/support/gwas_lookup/data/demo_rs3798220.json
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_api/__init__.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_api/base_client.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_api/ensembl.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_api/eqtl_catalogue.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_api/finngen.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_api/gtex.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_api/gwas_catalog.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_api/open_targets.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_api/pheweb_bbj.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_api/pheweb_ukb.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_api/portaldev.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_core/__init__.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_core/normalise.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_core/report.py
src/dnakit/workflows/support/gwas_lookup/gwas_lookup_core/resolve.py
src/dnakit/workflows/support/omics_target_evidence_mapper/SKILL.md
src/dnakit/workflows/support/omics_target_evidence_mapper/__init__.py
src/dnakit/workflows/support/omics_target_evidence_mapper/omics_target_evidence_mapper.py
src/dnakit/workflows/support/omics_target_evidence_mapper/examples/demo_input.json
src/dnakit/workflows/support/omics_target_evidence_mapper/examples/expected_output.md