bio-gene-callinglisted

# 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 (SSU 18S), RF02543 (LSU 28S), RF00002 (5.8S), RF00001 (5S). - Metazoan mitochondria, when applicable: RF02555 (12S), RF02546 (16S). `cmsearch --rfam --cut_ga --nohmmonly` is a sensible default; if no hits, rerun without `--cut_ga` and record both results. 4. For