bio-gene-calling
Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-gene-calling --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Bio Gene Calling Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes. ## Instructions 1. Select gene caller by organism class: - Prokaryotes and viruses (including giant viruses): **pyrodigal-gv** v0.3+ (SIMD-accelerated Cython bindings around prodigal-gv; same model set, much faster, actively maintained). - Eukaryotes: **BRAKER3** (*Genome Research* 2024, DOI: 10.1101/gr.278090.123) as the fully-automated pipeline. BRAKER3 invokes AUGUSTUS internally; do not run AUGUSTUS as a standalone caller. 2. Run gene calling and produce GFF/FAA/FNA. 3. Always run tRNA detection and rRNA detection on every assembly, and report counts per class. Negative findings (zero hits at default and relaxed thresholds) are required results — never leave ncRNA presence/absence unstated. - tRNA: tRNAscan-SE v2.0.12+ (preferred; isotype-specific covariance models) or ARAGORN v1.2.41+ for tmRNA where appropriate. - rRNA: Infernal v1.1.5+ `cmsearch` against the relevant Rfam covariance models. Pick the model set by domain of life: - Bacteria: RF00177 (SSU 16S), RF02541 (LSU 23S), RF00001 (5S). - Archaea: RF01959 (SSU 16S), RF02540 (LSU 23S), RF00001 (5S). - Eukaryotes: RF01960 (S
- Instructions
- Quick Reference
- Input Requirements
- Output
- Quality Gates
- Examples
- Example 1: Expected input layout
- Troubleshooting
What does the bio-gene-calling skill do?
Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-gene-calling --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.