Bio Gene Calling
Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.
Instructions
- Select gene caller by organism class.
- Run gene calling and produce GFF/FAA/FNA.
- Detect tRNAs/rRNAs if requested.
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. - Input contigs or bins are available. Inputs:
- contigs.fasta or bins/*.fasta
Output
- results/bio-gene-calling/genes.gff3
- results/bio-gene-calling/proteins.faa
- results/bio-gene-calling/cds.fna
- results/bio-gene-calling/gene_metrics.tsv
- results/bio-gene-calling/logs/
Quality Gates
- Gene count sanity checks pass.
- Start/stop codon checks pass.
- On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
- Verify contigs are non-empty and DNA alphabet.
- Verify outputs contain expected feature types.
Examples
Example 1: Expected input layout
contigs.fasta or bins/*.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.