Bio Viromics

When to use

• Detect, classify, and QC viral contigs.

Prerequisites

• Tools installed via pixi (see pixi.toml).
• Reference DB root: /media/shared-expansion/db/ (wsu; override per machine branch).
• Input contigs are available.

Inputs

• contigs.fasta

Outputs

• results/bio-viromics/viral_contigs.fasta
• results/bio-viromics/checkv_results/
• results/bio-viromics/vcontact3_results/
• results/bio-viromics/viral_taxonomy.tsv
• results/bio-viromics/genome_clusters.tsv
• results/bio-viromics/viromics_report.md
• results/bio-viromics/logs/

Steps

1. Run virus detection (geNomad).
2. Run CheckV for completeness/contamination.
3. Assign taxonomy and cluster genomes (vConTACT3 for hierarchical classification and gene-sharing network analysis).

QC gates

• CheckV quality thresholds meet project standards.
• Contamination flags are below thresholds.
• On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.

Validation

• Verify contigs.fasta is non-empty.
• Verify viral reference DBs exist under the reference root.

Tools

• genomad v1.11.2
• checkv v1.0.3
• vcontact3 v3.0.1
• gvclass v1.2.0 (internal build tag)

Paper summaries (2023-2025)

• summaries/ (include example use cases and tool settings used)

Tool documentation

• geNomad - Viral sequence identification and classification
• CheckV - Viral genome quality assessment
• vConTACT3 - Viral taxonomy and clustering via gene-sharing networks
• GVClass - Giant virus classification

References

• See ../bio-skills-references.md