AUGUSTUS

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be used as an ab initio predictor and can also incorporate external evidence such as RNA-Seq alignments and protein homology.

AUGUSTUS

License

Free to use and open source under the Artistic License 1.0.

Available

Roihu: 3.5.0, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load augustus/3.5.0

To predict genes using an existing species model:

augustus --species=human genome.fa > predictions.gff

Configuration directory

The module sets the AUGUSTUS_CONFIG_PATH environment variable, pointing to the configuration directory (species models, parameters) in the module installation. This installation is read-only, which is fine for running predictions with existing species models.

If you need to train a new species (or otherwise write to the configuration directory, for example with etraining or the autoAug scripts), copy the configuration to a writable location and point AUGUSTUS_CONFIG_PATH there:

cp -r $AUGUSTUS_CONFIG_PATH /scratch/<project>/augustus_config
export AUGUSTUS_CONFIG_PATH=/scratch/<project>/augustus_config

Example batch script

#!/bin/bash
#SBATCH --job-name=augustus
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=8G

module load bio-apps/v202603
module load augustus/3.5.0

augustus --species=human genome.fa > predictions.gff

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