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Bio Viromics
bio-viromics
Detect, classify, and QC viral contigs.
SKILL.md
Full skill instructions
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
- Run virus detection (geNomad).
- Run CheckV for completeness/contamination.
- 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
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