LICENSE
README.md
pyproject.toml
bacpage/__init__.py
bacpage/command.py
bacpage.egg-info/PKG-INFO
bacpage.egg-info/SOURCES.txt
bacpage.egg-info/dependency_links.txt
bacpage.egg-info/entry_points.txt
bacpage.egg-info/requires.txt
bacpage.egg-info/top_level.txt
bacpage/resources/__init__.py
bacpage/resources/cholera_gubbins_mask.gff
bacpage/resources/cholera_mask.gff
bacpage/resources/multiqc_config.yaml
bacpage/resources/vc_reference.fasta
bacpage/resources/cholera_ref_genes/ctxA.fasta
bacpage/resources/cholera_ref_genes/tcpA_classical.fasta
bacpage/resources/cholera_ref_genes/tcpA_eltor.fasta
bacpage/resources/cholera_ref_genes/toxR.fasta
bacpage/resources/cholera_ref_genes/wbeO1.fasta
bacpage/resources/cholera_ref_genes/wbfO139.fasta
bacpage/rules/__init__.py
bacpage/rules/assemble.smk
bacpage/rules/denovo.smk
bacpage/rules/phylogeny.smk
bacpage/rules/profiling.smk
bacpage/rules/quality-control.smk
bacpage/schemas/Illumina_config.schema.yaml
bacpage/schemas/Illumina_metadata.schema.yaml
bacpage/schemas/__init__.py
bacpage/schemas/illumina_config.template.yaml
bacpage/scripts/__init__.py
bacpage/scripts/calculate_typing_stats.py
bacpage/scripts/plot_coverage.py
bacpage/src/__init__.py
bacpage/src/assemble.py
bacpage/src/common_funcs.py
bacpage/src/example.py
bacpage/src/identify.py
bacpage/src/phylogeny.py
bacpage/src/profiling.py
bacpage/src/version.py
test/test_assemble.py
test/test_example.py
test/test_identify.py
test/test_phylogeny.py
test/test_profile.py