prodigal

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