BRAKER is a tool for eukaryotic genome annotation. It uses genomic and RNA-Seq data to automatically generate full gene structure annotations in novel genome. BRAKER is based on GeneMark-ET R2 and AUGUSTUS pipelines.


Free to use and open source under [Artistic License] (


Version on CSC's Servers

Puhti: 2.1.6


In Puhti BRAKER should be used only in batch jobs. Either in normal batch jobs or in interactive batch jobs.

Interactive usage

You can start interactive batch job with command:

sinteractive -i
BRAKER can utilize several computing cores and can require significant amount of memory so you should reserve more than the default resources for your interactive batch job. For example 4 cores and 32 GB of memory.

In batch job, you can initialize BRAKER environment with command

module load braker
After that you can launch a BRAKER job with command:


This command should be used in stead of the original script, as it automatically sets some parameters that enable running BRAKER in Puhti. braker-puhti is able to use all the command line options of To see the options, run command:

braker-puhti --help
Sample BRAKER command in Puhti:

 braker-puhti --species=sp1 --genome=Drosophila.dna.fa --prot_seq=Drosophila.pep.fa --prg=gth --trainFromGth --AUGUSTUS_ab_initio --cores=$SLURM_CPUS_PER_TASK

Batch jobs

Sample batch job scrip for BRAKER:

#SBATCH --job-name=BRAKER_Job
#SBATCH --account=project_2012345
#SBATCH --time=24:00:00
#SBATCH --mem=32000
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8  
#SBATCH --partition=small

# load braker
module load braker

# start the job
braker-puhti --species=sp1 --genome=Drosophila.dna.fa --prot_seq=Drosophila.pep.fa \
--prg=gth --trainFromGth --AUGUSTUS_ab_initio --cores=$SLURM_CPUS_PER_TASK

In the batch job example above one task (--ntasks 1) is executed. The BRAKER job uses 8 cores (--cpus-per-task=8 ) with total of 32 GB of memory (--mem=32000). The maximum duration of the job is ten hours (--time 10:00:00 ). All the cores are assigned from one computing node (--nodes=1 ). In the example the project that will be used is project_2012345. This value shuold be replaced by the name of your computing project.

You can submit the batch job file to the batch job system with command:

sbatch batch_job_file.bash
See the Puhti user guide for more information about running batch jobs.

More information

Last edited Wed Jul 6 2022