majiayu000 Bio Gene Calling
When to use
- Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.
Prerequisites
- Tools installed via pixi (see pixi.toml).
- Input contigs or bins are available.
Inputs
- contigs.fasta or bins/*.fasta
Outputs
- 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/
Steps
- Select gene caller by organism class.
- Run gene calling and produce GFF/FAA/FNA.
- Detect tRNAs/rRNAs if requested.
QC 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.
Validation
- Verify contigs are non-empty and DNA alphabet.
- Verify outputs contain expected feature types.
Tools
- pyrodigal v3.7.0
- prodigal-gv v2.11.0
- braker v3.0.8
- augustus v3.5.0
- trnascan-se v2.0.12
Paper summaries (2023-2025)
- summaries/ (include example use cases and tool settings used)
Tool documentation
- Pyrodigal - Fast prokaryotic gene prediction
- Prodigal-gv - Gene prediction for giant viruses
- BRAKER - Eukaryotic gene prediction pipeline
- AUGUSTUS - Eukaryotic gene prediction
- tRNAscan-SE - Transfer RNA gene detection
References
- See ../bio-skills-references.md