LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
viralunity/__init__.py
viralunity/_orchestrator.py
viralunity/_subprocess.py
viralunity/config_generator.py
viralunity/constants.py
viralunity/exceptions.py
viralunity/logging_config.py
viralunity/provenance.py
viralunity/validators.py
viralunity/viralunity_build_deacon_index_cli.py
viralunity/viralunity_cli.py
viralunity/viralunity_consensus.py
viralunity/viralunity_consensus_cli.py
viralunity/viralunity_create_samplesheet.py
viralunity/viralunity_get_databases_cli.py
viralunity/viralunity_meta.py
viralunity/viralunity_meta_cli.py
viralunity/viralunity_setup_cli.py
viralunity.egg-info/PKG-INFO
viralunity.egg-info/SOURCES.txt
viralunity.egg-info/dependency_links.txt
viralunity.egg-info/entry_points.txt
viralunity.egg-info/requires.txt
viralunity.egg-info/top_level.txt
viralunity/scripts/__init__.py
viralunity/scripts/consensus_illumina.smk
viralunity/scripts/consensus_illumina_segmented.smk
viralunity/scripts/consensus_nanopore.smk
viralunity/scripts/consensus_nanopore_segmented.smk
viralunity/scripts/metagenomics_illumina.smk
viralunity/scripts/metagenomics_nanopore.smk
viralunity/scripts/envs/alignment.yaml
viralunity/scripts/envs/assembly.yaml
viralunity/scripts/envs/clair3.yaml
viralunity/scripts/envs/consensus.yaml
viralunity/scripts/envs/genome_selection.yaml
viralunity/scripts/envs/medaka.yaml
viralunity/scripts/envs/qc.yaml
viralunity/scripts/envs/taxonomy.yaml
viralunity/scripts/envs/utils.yaml
viralunity/scripts/python/__init__.py
viralunity/scripts/python/add_RPM_to_summary.py
viralunity/scripts/python/add_negative_control_enrichment.py
viralunity/scripts/python/add_rpkm_to_summary.py
viralunity/scripts/python/annotate_diamond_taxonomy.py
viralunity/scripts/python/annotate_nr_taxonomy.py
viralunity/scripts/python/apply_ictv_host_filter.py
viralunity/scripts/python/apply_max_rpm_bleed_filter.py
viralunity/scripts/python/build_genome_length_table.py
viralunity/scripts/python/build_ictv_vertebrate_taxids.py
viralunity/scripts/python/calculate_assembly_stats.py
viralunity/scripts/python/combine_contigs.py
viralunity/scripts/python/convert_diamond_output_to_krona_input.py
viralunity/scripts/python/filter_diamond_by_idxstats.py
viralunity/scripts/python/filter_krona_by_pass_taxids.py
viralunity/scripts/python/filter_taxids.py
viralunity/scripts/python/filter_top_species_hits.py
viralunity/scripts/python/harmonize_nr_summary.py
viralunity/scripts/python/rename_sequences.py
viralunity/scripts/python/select_reference_genomes.py
viralunity/scripts/python/split_search_output.py
viralunity/scripts/python/summarize_krona_taxa.py
viralunity/scripts/python/taxonomy.py
viralunity/scripts/rules/__init__.py
viralunity/scripts/rules/alignment_illumina.smk
viralunity/scripts/rules/alignment_nanopore.smk
viralunity/scripts/rules/consensus_illumina.smk
viralunity/scripts/rules/consensus_illumina_common.smk
viralunity/scripts/rules/consensus_nanopore.smk
viralunity/scripts/rules/consensus_nanopore_common.smk
viralunity/scripts/rules/metagenomics_assembly_illumina.smk
viralunity/scripts/rules/metagenomics_assembly_nanopore.smk
viralunity/scripts/rules/metagenomics_dehost_illumina.smk
viralunity/scripts/rules/metagenomics_dehost_nanopore.smk
viralunity/scripts/rules/metagenomics_diamond_contigs_illumina.smk
viralunity/scripts/rules/metagenomics_diamond_contigs_nanopore.smk
viralunity/scripts/rules/metagenomics_diamond_reads_illumina.smk
viralunity/scripts/rules/metagenomics_diamond_reads_nanopore.smk
viralunity/scripts/rules/metagenomics_genome_lengths.smk
viralunity/scripts/rules/metagenomics_kraken2_contigs_illumina.smk
viralunity/scripts/rules/metagenomics_kraken2_contigs_nanopore.smk
viralunity/scripts/rules/metagenomics_kraken2_reads_illumina.smk
viralunity/scripts/rules/metagenomics_kraken2_reads_nanopore.smk
viralunity/scripts/rules/metagenomics_multiqc_illumina.smk
viralunity/scripts/rules/metagenomics_nr_validation_illumina.smk
viralunity/scripts/rules/metagenomics_nr_validation_nanopore.smk
viralunity/scripts/rules/metagenomics_reference_assembly.smk
viralunity/scripts/rules/qc_illumina.smk
viralunity/scripts/rules/stats.smk