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Viral / plasmid track

A per-sample viral and plasmid discovery track that runs parallel to the MAG track and does not touch it. It is opt-in: run_magmaker.sh does not run it, and it is requested as its own Stage 3 target.

snakemake --snakefile Snakefile-bin --profile resources/profiles/demon virus_all \
  --config binning=output/config/auto_binning.txt

What it does

per-sample contigs → geNomad end-to-end → viral contigs + plasmid contigs
viral contigs → CheckV → completeness / contamination
→ output/virus/virus_summary.tsv
  • geNomad (run_genomad) classifies viral and plasmid contigs straight from each assembly. No read mapping is needed, so this branch depends only on the assemblies from Stage 1 — it can run before, during or after the MAG track.
  • CheckV (run_checkv) scores completeness and contamination for the viral contigs geNomad called. It skips cleanly when a sample has none.
  • make_virus_summary merges every sample's geNomad and CheckV output into one table.

geNomad's own --cleanup is deliberately not used — it races NFS silly-rename on shared storage and exits non-zero after the real outputs are already written. The rule lets geNomad finish and then removes the heavy module intermediates itself, keeping the *_summary directory downstream rules read.

Configuration

params:
  genomad:
    db_path: /path/to/genomad_db      # genomad download-database <dir>
    extra: ''                          # e.g. --conservative for higher-precision calls
  checkv:
    db_path: /path/to/checkv-db-v1.5  # checkv download_database <dir>

See Database setup for how to download both.

Output

output/virus/:

genomad/{assembler}/{sample}/    geNomad per-sample output (summary dir kept, intermediates removed)
checkv/{assembler}/{sample}/     CheckV quality for the viral contigs
virus_summary.tsv                merged table, one row per viral or plasmid contig

virus_summary.tsv columns — see the Viral summary table section of Output. In short: geNomad contig stats and score for every row, geNomad viral taxonomy on virus rows, geNomad plasmid annotations (Conjugation_Genes, AMR_Genes) on plasmid rows, and CheckV quality / completeness / contamination joined onto the virus rows. CheckV does not score plasmids, so those fields are blank there.

Scope

This is a per-sample track. Dereplicating viruses into vOTUs across samples (95% ANI / 85% AF, MIUViG) is a downstream cross-sample analysis choice, kept out of MAGmaker for the same reason dRep is — it is not part of per-sample genome recovery.

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