.gitignore
LICENSE.txt
MANIFEST.in
Makefile
README.md
conf-private.yml
conf.yml
environment.yml
hash-upsetr-example.ipynb
mkdocs.yml
setup.cfg
setup.py
snakemake.slurm
.github/workflows/test.yml
doc/configuring.md
doc/gather-vs-mapping.pdf
doc/gather-vs-mapping.png
doc/index.md
doc/quickstart.md
genome_grist/__init__.py
genome_grist/__main__.py
genome_grist/combine_csvs.py
genome_grist/copy_local_genomes.py
genome_grist/genbank_genomes.py
genome_grist/make_info_file.py
genome_grist/subtract_gather.py
genome_grist/summarize_gather_hashes.py
genome_grist/summarize_mapping.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-gather.ipynb
genome_grist/notebooks/report-mapping.ipynb
genome_grist/notebooks/report-taxonomy.ipynb
inputs/adapters.fa
tests/__init__.py
tests/pytest_utils.py
tests/test_snakemake.py
tests/test-data/SRR5950647-genomes.info.csv
tests/test-data/SRR5950647.conf
tests/test-data/SRR5950647.x.gtdb-rs202.matches.zip
tests/test-data/SRR5950647.x.gtdb.csv
tests/test-data/SRR5950647_picklist.conf
tests/test-data/SRR5950647_picklist.picklist.csv
tests/test-data/SRR5950647_subset.abundtrim.fq.gz
tests/test-data/SRR5950647_subset.conf
tests/test-data/SRR5950647_subset.tax.csv
tests/test-data/bad-1.conf
tests/test-data/bad-2.conf
tests/test-data/bad-3.conf
tests/test-data/bad-4.conf
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
tests/test-data/SRR5950647-genomes/GCF_003697165.2.info.csv
tests/test-data/SRR5950647-genomes/GCF_003697165.2_genomic.fna.gz
tests/test-data/SRR5950647-genomes/GCF_902167755.1.info.csv
tests/test-data/SRR5950647-genomes/GCF_902167755.1_genomic.fna.gz