bio-viromics

Original：🇺🇸 English

Translated

Detect, classify, and QC viral contigs.

1installs

Added on2026-02-20

NPX Install

npx skill4agent add fmschulz/omics-skills bio-viromics

Detect, classify, and QC viral contigs.

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

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

Prerequisites:

Tools available in the active environment (Pixi/conda/system). See
```
docs/README.md
```
for expected tools.
Reference DB root: set
```
BIO_DB_ROOT
```
(default
```
/media/shared-expansion/db/
```
on WSU).
Input contigs are available. Inputs:
contigs.fasta

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.

text

contigs.fasta

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.