LICENSE
MANIFEST.in
README.md
setup.py
koverage/CITATION
koverage/VERSION
koverage/__init__.py
koverage/__main__.py
koverage.egg-info/PKG-INFO
koverage.egg-info/SOURCES.txt
koverage.egg-info/dependency_links.txt
koverage.egg-info/entry_points.txt
koverage.egg-info/requires.txt
koverage.egg-info/top_level.txt
koverage/config/config.yaml
koverage/config/system_config.yaml
koverage/scripts/__init__.py
koverage/scripts/combineCoverage.py
koverage/scripts/combineKmerCoverage.py
koverage/scripts/kmerScreen.py
koverage/scripts/koverageReport.py
koverage/scripts/minimapWrapper.py
koverage/scripts/refSampleKmer.py
koverage/scripts/sampleCoverage.py
koverage/test_data/ref.fa
koverage/test_data/reads/A13-04-182-06_TAGCTT_R1.fastq.gz
koverage/test_data/reads/A13-04-182-06_TAGCTT_R2.fastq.gz
koverage/test_data/reads/A13-151-169-06_ATGTCA_R1.fastq.gz
koverage/test_data/reads/A13-151-169-06_ATGTCA_R2.fastq.gz
koverage/test_data/refs/ref1.fa.gz
koverage/test_data/refs/ref2.fa.gz
koverage/test_data/refs/ref3.fa.gz
koverage/test_data/refs/ref4.fa.gz
koverage/test_data/refs/refs.tsv
koverage/workflow/Snakefile
koverage/workflow/__init__.py
koverage/workflow/envs/coverm.yaml
koverage/workflow/envs/jellyfish.yaml
koverage/workflow/envs/minimap.yaml
koverage/workflow/envs/zstd.yaml
koverage/workflow/rules/__init__.py
koverage/workflow/rules/combine_refs.smk
koverage/workflow/rules/coverage.smk
koverage/workflow/rules/coverm.smk
koverage/workflow/rules/kmer_coverage.smk
koverage/workflow/rules/preflight.smk
koverage/workflow/rules/reports.smk
tests/test_combineCoverage.py
tests/test_combineKmerCoverage.py
tests/test_kmerScreen.py
tests/test_koverage.py
tests/test_minimapWrapper.py
tests/test_refSampleKmer.py
tests/test_sampleCoverage.py