Bio Gene Calling

Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.

Instructions

1. Select gene caller by organism class.
2. Run gene calling and produce GFF/FAA/FNA.
3. 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.