├── .github └── workflows │ └── test.yml ├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── bak └── test-data │ ├── 00-test.conf │ ├── genome_list.txt │ ├── genomes │ ├── 47.fa.gz │ └── chimeric.fa.gz │ ├── podar-ref.lca.json.gz │ └── provided-lineages.csv ├── charcoal ├── Snakefile ├── Snakefile.download_db ├── __init__.py ├── __main__.py ├── alignplot.py ├── clean_genome.py ├── combine_csvs.py ├── compare_taxonomy.py ├── conf │ ├── defaults.conf │ ├── env-genbank.yml │ ├── env-mashmap.yml │ ├── env-mummer.yml │ ├── env-reporting.yml │ ├── env-sourmash.yml │ └── system.conf ├── contigs_list_contaminants.py ├── contigs_search_taxonomy.py ├── figs │ ├── __init__.py │ └── sourmash_sankey.py ├── genbank_genomes.py ├── just_taxonomy.py ├── lineage_db.py ├── notebooks │ ├── explore-contam.ipynb │ ├── report-alignment.ipynb │ ├── report-genome.ipynb │ ├── report-index.ipynb │ └── report-stage2.ipynb ├── postprocess_alignments.py └── utils.py ├── conf ├── gtdb-contam-dna.conf ├── ibd2.conf ├── ibd2.provided_lineages ├── ibd2 │ └── genome-list.txt ├── tara-delmont-all-list.txt ├── tara-delmont-provided-lineages.csv └── tara-delmont.conf ├── demo ├── GCA_001593925.sig.gz ├── LoombaR_2017__SID1050_bax__bin.11.fa.gz.gather-matches.sig.gz ├── README.md ├── TARA_ANE_MAG_00014.fa.gather-matches.sig.gz ├── TARA_PON_MAG_00084.fa.gather-matches.sig.gz ├── demo-lineages.csv ├── demo.conf ├── demo.genome-list.txt ├── demo.prot-lineages.csv ├── demo.prot.conf ├── genomes │ ├── GCA_001593925.1_ASM159392v1_genomic.fna.gz │ ├── GCF_000005845-subset.fa.gz │ ├── LoombaR_2017__SID1050_bax__bin.11.fa.gz │ ├── TARA_ANE_MAG_00014.fa.gz │ ├── TARA_PON_MAG_00084.fa.gz │ ├── TOBG_NAT-167.fna.gz │ └── VatanenT_2016__G80294__bin.12.fna.gz └── provided-lineages.csv ├── doc ├── CODE_OF_CONDUCT.rst └── README.md ├── environment.yml ├── eval ├── almeida-eval.ipynb ├── tara-delmont-eval.ipynb ├── tara-delmont-relaxed.conf └── tara-delmont-strict.conf ├── example-output ├── LoombaR_2017__SID1050_bax__bin.11.fa.gz.report.txt ├── SRS104400_110.fna.gz.report.txt ├── TARA_ANE_MAG_00014.fa.gz.report.txt ├── almeida.combined_summary.csv ├── combined_summary.csv ├── demo.combined_summary.csv ├── ibd2.combined_summary.csv ├── quickstart.combined_summary.csv ├── tara.combined_summary.csv └── update.sh ├── post-summarize.py ├── pytest.ini ├── setup.py ├── snakemake.slurm ├── stats ├── stats.10000.txt ├── stats.5000.txt ├── stats.ipynb ├── stats10k.png └── stats5k.png └── tests ├── __init__.py ├── pytest_utils.py ├── test-data ├── 2.fa.gz.gather-matches.csv ├── 2.fa.gz.gather-matches.sig.gz ├── 2.fa.gz.gather-matches.zip ├── 63.fa.gz.gather-matches.sig.gz ├── GCA_001593925_hit-list.csv ├── genomes │ ├── 2.fa.gz │ ├── 2.fa.gz.sig │ ├── 63.fa.gz │ └── 63.fa.gz.sig ├── loomba-hit-list.csv ├── loomba │ ├── LoombaR_2017__SID1050_bax__bin.11.fa.gz.contigs-tax.json │ ├── LoombaR_2017__SID1050_bax__bin.11.fa.gz.matches.abund.zip │ ├── 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