LICENSE
MANIFEST.in
README.md
environment.yml
pyproject.toml
requirements.txt
setup.py
config/config.yaml
config/.ipynb_checkpoints/config-checkpoint.yaml
resources/barcode_reference_cleaned.fasta
resources/reference.fasta
resources/.ipynb_checkpoints/barcode_reference_cleaned-checkpoint.fasta
resources/.ipynb_checkpoints/reference-checkpoint.fasta
src/__init__.py
src/ngs_ai_agent.py
src/.ipynb_checkpoints/ngs_ai_agent-checkpoint.py
src/ai_orchestrator/__init__.py
src/ai_orchestrator/ollama_client.py
src/ai_orchestrator/.ipynb_checkpoints/ollama_client-checkpoint.py
src/ngs_ai_agent/__init__.py
src/ngs_ai_agent/cli.py
src/ngs_ai_agent/core.py
src/ngs_ai_agent.egg-info/PKG-INFO
src/ngs_ai_agent.egg-info/SOURCES.txt
src/ngs_ai_agent.egg-info/dependency_links.txt
src/ngs_ai_agent.egg-info/entry_points.txt
src/ngs_ai_agent.egg-info/not-zip-safe
src/ngs_ai_agent.egg-info/requires.txt
src/ngs_ai_agent.egg-info/top_level.txt
src/ngs_ai_agent/ai_orchestrator/__init__.py
src/ngs_ai_agent/ai_orchestrator/ollama_client.py
src/ngs_ai_agent/ai_orchestrator/.ipynb_checkpoints/ollama_client-checkpoint.py
workflow/rules/barcode_dms.smk
workflow/rules/direct_amplicon_dms.smk
workflow/rules/dms_analysis.smk
workflow/rules/mapping.smk
workflow/rules/qc.smk
workflow/rules/trimming.smk
workflow/rules/variant_calling.smk
workflow/rules/visualization.smk
workflow/rules/.ipynb_checkpoints/barcode_dms-checkpoint.smk
workflow/rules/.ipynb_checkpoints/direct_amplicon_dms-checkpoint.smk
workflow/rules/.ipynb_checkpoints/dms_analysis-checkpoint.smk
workflow/rules/.ipynb_checkpoints/mapping-checkpoint.smk
workflow/rules/.ipynb_checkpoints/qc-checkpoint.smk
workflow/rules/.ipynb_checkpoints/trimming-checkpoint.smk
workflow/rules/.ipynb_checkpoints/variant_calling-checkpoint.smk
workflow/rules/.ipynb_checkpoints/visualization-checkpoint.smk
workflow/scripts/barcode_qc_report.py
workflow/scripts/build_barcode_map_from_alignment.py
workflow/scripts/calculate_barcode_fitness.py
workflow/scripts/calculate_barcode_fitness_v2.py
workflow/scripts/count_barcodes.py
workflow/scripts/create_heatmap.py
workflow/scripts/dms_fitness.py
workflow/scripts/fitness_calculator.py
workflow/scripts/fitness_plots.py
workflow/scripts/generate_ai_report.py
workflow/scripts/variant_annotation.py
workflow/scripts/variant_caller.py
workflow/scripts/.ipynb_checkpoints/barcode_qc_report-checkpoint.py
workflow/scripts/.ipynb_checkpoints/build_barcode_map_from_alignment-checkpoint.py
workflow/scripts/.ipynb_checkpoints/calculate_barcode_fitness-checkpoint.py
workflow/scripts/.ipynb_checkpoints/count_barcodes-checkpoint.py
workflow/scripts/.ipynb_checkpoints/create_heatmap-checkpoint.py
workflow/scripts/.ipynb_checkpoints/fitness_calculator-checkpoint.py
workflow/scripts/.ipynb_checkpoints/generate_ai_report-checkpoint.py
workflow/scripts/.ipynb_checkpoints/variant_annotation-checkpoint.py
workflow/scripts/.ipynb_checkpoints/variant_caller-checkpoint.py