AUGUSTUS

Introduction

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.

For more information, please check its website: https://bioinf.uni-greifswald.de/augustus/.

Versions

  • 3.4.0

  • 3.5.0

Commands

  • aln2wig

  • augustus

  • bam2wig

  • bam2wig-dist

  • consensusFinder

  • curve2hints

  • etraining

  • fastBlockSearch

  • filterBam

  • getSeq

  • getSeq-dist

  • homGeneMapping

  • joingenes

  • prepareAlign

Module

You can load the modules by:

module load biocontainers
module load augustus/3.4.0

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run AUGUSTUS on our cluster:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=AUGUSTUS
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers augustus/3.4.0

augustus --species=botrytis_cinerea genome.fasta > annotation.gff