.git_archival.txt
.gitattributes
.gitignore
CHANGELOG.md
README.md
bandit.yaml
pyproject.toml
.github/workflows/continuous_integration.yaml
data/hq_decont_reads.fastq
data/raw_reads.fastq.gz
data/test_db/names.dmp.gz
data/test_db/nodes.dmp.gz
data/test_db/viral_nuccore/viral_accn_taxid.dmp
data/test_db/viral_nuccore/viral_database.fasta
data/test_db/viral_nuccore/viral_db.ndb
data/test_db/viral_nuccore/viral_db.nhd
data/test_db/viral_nuccore/viral_db.nhi
data/test_db/viral_nuccore/viral_db.nhr
data/test_db/viral_nuccore/viral_db.nin
data/test_db/viral_nuccore/viral_db.njs
data/test_db/viral_nuccore/viral_db.nog
data/test_db/viral_nuccore/viral_db.nos
data/test_db/viral_nuccore/viral_db.not
data/test_db/viral_nuccore/viral_db.nsq
data/test_db/viral_nuccore/viral_db.ntf
data/test_db/viral_nuccore/viral_db.nto
data/test_db/viral_nuccore/viral_seqs_info.tsv
documentation/mkdocs.yml
documentation/docs/Covplot.md
documentation/docs/Installation.md
documentation/docs/Preparation.md
documentation/docs/Wolfpack.md
documentation/docs/index.md
documentation/docs/assets/coverage_example.png
documentation/docs/assets/logo.svg
src/scripts/allorgs_covplot.py
src/scripts/parse_bact_fung_reads.py
src/scripts/treemap.R
src/virmet/__init__.py
src/virmet/__main__.py
src/virmet/cli.py
src/virmet/common.py
src/virmet/covplot.R
src/virmet/covplot.py
src/virmet/fetch.py
src/virmet/index.py
src/virmet/tidytable.py
src/virmet/update.py
src/virmet/wolfpack.py
src/virmet.egg-info/PKG-INFO
src/virmet.egg-info/SOURCES.txt
src/virmet.egg-info/dependency_links.txt
src/virmet.egg-info/entry_points.txt
src/virmet.egg-info/requires.txt
src/virmet.egg-info/top_level.txt
tests/__init__.py
tests/__main__.py
tests/test_common.py
tests/test_covplot.py
tests/test_ext_tools.py
tests/test_wolfpack.py