Bio Gene Calling

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

Instructions

Tool guides and versions: docs/README.md.

1. Validate the assembly and tool manifests, then generate a per-assembly execution plan:

   uv run --script skills/bio-gene-calling/scripts/run_gene_calling.py \
     assemblies.tsv --tool-manifest tool-manifest.json \
     --out results/bio-gene-calling
   # Inspect run_manifest.json, then execute or resume the same plan:
   uv run --no-project python skills/bio-gene-calling/scripts/run_gene_calling.py \
     assemblies.tsv --tool-manifest tool-manifest.json \
     --out results/bio-gene-calling --execute