| name | prodigal |
| description | Protein-coding gene prediction; use -p meta for metagenomes. Use this skill when working with prodigal: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/hyattpd/Prodigal. For routing across tools, use tool-selection. For end-to-end pipelines, use metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["genes","orf"] |
| upstream | https://github.com/hyattpd/Prodigal |
Prodigal
Upstream: hyattpd/Prodigal
Citation
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010). https://doi.org/10.1186/1471-2105-11-119
See also docs/references.md.
Analytical thinking
For metagenomes always use -p meta. Gene catalogues inherit assembly
errors—garbage contigs produce garbage ORFs. Optionally keep only complete genes
(partial=00) when catalogs are huge.
How to run
prodigal -i contigs.fa \
-d genes.fna -a genes.faa \
-o genes.gff -p meta -f gff
Decision tree
Have contigs?
├─ Build gene catalogue → prodigal → cd-hit → salmon → eggnog-mapper
└─ Only MAGs → predict genes per MAG later for annotation
Related skills
megahit · cd-hit · salmon · eggnog-mapper
