BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes.

For more information. please check its github repository


  • 2.1.6


Helper command


Since BRAKER is a pipeline that trains AUGUSTUS, i.e. writes species specific parameter files, BRAKER needs writing access to the configuration directory of AUGUSTUS that contains such files. This installation comes with a stub of AUGUSTUS coniguration files, but you must copy them out from the container into a location where you have write permissions.

A helper command copy_augustus_config is provided to simplify the task. Follow the procedure below to put the config files in your scratch space:

$ mkdir -p $RCAC_SCRATCH/augustus
$ copy_augustus_config $RCAC_SCRATCH/augustus
$ export AUGUSTUS_CONFIG_PATH=$RCAC_SCRATCH/augustus/config


You can load the modules by:

module load biocontainers
module load braker2/2.1.6

Example job


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 BRAKER on our cluster:

#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -n 24
#SBATCH --job-name=BRAKER2
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers braker2/2.1.6

# The augustus config step is only required for the first time to use BRAKER2
mkdir -p $RCAC_SCRATCH/augustus
copy_augustus_config $RCAC_SCRATCH/augustus
export AUGUSTUS_CONFIG_PATH=$RCAC_SCRATCH/augustus/config --genome genome.fa --bam RNAseq.bam --softmasking --cores 24