Skip to content

BRAKER

Description

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.

License

Free to use and open source under [Artistic License] (https://opensource.org/licenses/artistic-license-1.0)

Version

Version on CSC's Servers

Puhti: 2.1.6

Usage

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:

braker-puhti

This command should be used in stead of the original braker.pl 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 braker.pl. 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:

#!/bin/bash
#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 update: October 10, 2022