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.md for 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.