Prodigal

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a fast, reliable protein-coding gene prediction tool for prokaryotic (bacterial and archaeal) genomes.

Prodigal

License

Free to use and open source under GNU GPLv3.

Available

Roihu: 2.6.3, via the bio-apps module.

Usage

Prodigal is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Prodigal module:

module load bio-apps/v202603
module load prodigal/2.6.3

Predict genes from a genome, writing gene coordinates (GFF) and protein translations:

prodigal -i genome.fna -o genes.gff -f gff -a proteins.faa -d genes.fna

For metagenomic data, use the anonymous/meta procedure with -p meta.

Example batch script

#!/bin/bash
#SBATCH --job-name=prodigal
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=02:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G

module load bio-apps/v202603
module load prodigal/2.6.3

prodigal -i genome.fna -o genes.gff -f gff -a proteins.faa -d genes.fna

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk