bio-viromics
npx machina-cli add skill fmschulz/omics-skills/bio-viromics --openclawBio Viromics
Detect, classify, and QC viral contigs.
Instructions
- Run virus detection (geNomad).
- Run CheckV for completeness/contamination.
- Assign taxonomy and cluster genomes (vConTACT3 for hierarchical classification and gene-sharing network analysis).
Quick Reference
| Task | Action |
|---|---|
| Run workflow | Follow the steps in this skill and capture outputs. |
| Validate inputs | Confirm required inputs and reference data exist. |
| Review outputs | Inspect reports and QC gates before proceeding. |
| Tool docs | See docs/README.md. |
| References | - See ../bio-skills-references.md |
Input Requirements
Prerequisites:
- Tools available in the active environment (Pixi/conda/system). See
docs/README.mdfor expected tools. - Reference DB root: set
BIO_DB_ROOT(default/media/shared-expansion/db/on WSU). - Input contigs are available. Inputs:
- contigs.fasta
Output
- 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/
Quality 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.
- Verify contigs.fasta is non-empty.
- Verify viral reference DBs exist under the reference root.
Examples
Example 1: Expected input layout
contigs.fasta
Troubleshooting
Issue: Missing inputs or reference databases Solution: Verify paths and permissions before running the workflow.
Issue: Low-quality results or failed QC gates Solution: Review reports, adjust parameters, and re-run the affected step.
Source
git clone https://github.com/fmschulz/omics-skills/blob/main/skills/bio-viromics/SKILL.mdView on GitHub Overview
Bio Viromics detects viral contigs in assemblies, classifies them, and performs QC. It combines virome detection with geNomad, CheckV completeness/contamination checks, and taxonomy/clustering via vConTACT3 to produce a curated viral contig catalog and a comprehensive report.
How This Skill Works
Inputs come from contigs.fasta. The workflow runs geNomad for virus detection, then CheckV to assess completeness and contamination. Finally, taxonomy is assigned and genomes are clustered using vConTACT3, with outputs organized under results/bio-viromics.
When to Use It
- You have a contigs.fasta from a metagenomic assembly and need to identify viral contigs.
- You require quality control with CheckV to evaluate completeness and contamination.
- You want to assign taxonomy and cluster genomes for downstream analyses.
- You must validate inputs, reference data, and tool availability before running the workflow.
- You are preparing a viral contig set for reporting or downstream ecological analyses.
Quick Start
- Step 1: Run virus detection with geNomad on contigs.fasta.
- Step 2: Run CheckV to assess completeness and contamination.
- Step 3: Assign taxonomy and cluster with vConTACT3; review outputs under results/bio-viromics.
Best Practices
- Validate inputs exist and reference data is accessible (BIO_DB_ROOT and contigs.fasta).
- Ensure prerequisite tools are installed and discoverable (Pixi/conda/system) per docs.
- Review QC gates in CheckV results and verify contigs.fasta is non-empty.
- Inspect outputs (viral_contigs.fasta, checkv_results, vcontact3_results, taxonomy and clusters) before proceeding.
- Document parameters and re-run with adjusted settings if QC gates fail.
Example Use Cases
- Detect viral contigs in soil metagenomes and generate taxonomy
- Characterize marine virome contigs and cluster genomes
- Assess human gut viral contigs with completeness metrics
- Troubleshoot QC gates by adjusting parameters and re-running affected steps
- Create a final viral contig catalog for downstream ecological analyses
