.gitignore
LICENSE.txt
MANIFEST.in
Makefile
README.md
conf.yml
environment.yml
gather-p8808mo11.ipynb
gather-p8808mo9.ipynb
gather-podar.ipynb
gathergram.ipynb
hash-upsetr-example.ipynb
setup.cfg
setup.py
snakemake.slurm
.github/workflows/test.yml
genome_grist/__init__.py
genome_grist/__main__.py
genome_grist/combine_csvs.py
genome_grist/gather_split.py
genome_grist/genbank_genomes.py
genome_grist/subtract_gather.py
genome_grist/version.py
genome_grist.egg-info/PKG-INFO
genome_grist.egg-info/SOURCES.txt
genome_grist.egg-info/dependency_links.txt
genome_grist.egg-info/entry_points.txt
genome_grist.egg-info/requires.txt
genome_grist.egg-info/top_level.txt
genome_grist/conf/Snakefile
genome_grist/conf/defaults.conf
genome_grist/conf/system.conf
genome_grist/conf/env/bcftools.yml
genome_grist/conf/env/covtobed.yml
genome_grist/conf/env/minimap2.yml
genome_grist/conf/env/papermill.yml
genome_grist/conf/env/sourmash.yml
genome_grist/conf/env/sra.yml
genome_grist/conf/env/trim.yml
genome_grist/conf/env/wget.yml
genome_grist/notebooks/report-sample.ipynb
inputs/adapters.fa
tests/__init__.py
tests/pytest_utils.py
tests/test_snakemake.py
tests/test-data/HSMA33MX-GCA_001881345.1.fna.gz
tests/test-data/HSMA33MX-GCA_009494275.1.fna.gz
tests/test-data/HSMA33MX-subset.abundtrim.fq.gz
tests/test-data/HSMA33MX-subset.conf
tests/test-data/HSMA33MX-subset.genomes.accs.txt
tests/test-data/HSMA33MX-subset.genomes.info.csv
tests/test-data/HSMA33MX-subset.x.genbank.gather.csv
tests/test-data/HSMA33MX-subset.x.genbank.gather.out
tests/test-data/HSMA33MX-subset.x.genbank.matches.sig
tests/test-data/HSMA33MX.conf
tests/test-data/HSMA33MX.x.genbank.gather.csv
tests/test-data/twofoo-head.abundtrim.fq.gz
tests/test-data/twofoo-head.x.genbank.gather.csv
tests/test-data/twofoo-head.x.genbank.gather.sig