| name | prokka |
| description | Rapid prokaryotic genome annotation (CDS/rRNA/tRNA). Use this skill when working with prokka: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/tseemann/prokka. For stage routing use tool-selection / metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["annotation","orf","prokaryote"] |
| upstream | https://github.com/tseemann/prokka |
| stage | function |
Prokka
Upstream: Prokka
Citation
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014). https://doi.org/10.1093/bioinformatics/btu153
See also docs/references.md.
Analytical thinking
Prokka wraps Prodigal + feature predictors into GenBank/GFF — convenient for
per-genome annotation of isolates/MAGs. For large non-redundant gene
catalogues prefer prodigal → cd-hit/mmseqs2 → eggnog-mapper.
| Need | Prefer |
|---|
| Standardized bacterial annotation + modern DBs | bakta |
| Classic rapid GFF/GBK, minimal deps | prokka |
| Catalogue-scale ORFs only | prodigal |
Fragmented MAGs yield incomplete/wrong gene calls — filter with mag-qc first.
How to run
prokka bins/bin.fa --outdir temp/prokka/${id} --prefix ${id} --cpus 8 --force
Key parameters
| Flag | Notes |
|---|
--cpus | Threads |
--kingdom | Bacteria default; set Archaea when appropriate |
--compliant | NCBI-oriented outputs when submitting |
Decision tree
Annotate a bacterial/archaeal genome/MAG?
├─ Modern standardized → bakta
├─ Classic rapid GBK/GFF → prokka
└─ Only proteins for catalogue → prodigal
Related skills
bakta · prodigal · eggnog-mapper · barrnap · antismash · dram ·
tool-selection
