BRAKER3 is the latest pipeline in the BRAKER suite. It enables the usage of RNA-seq and protein data in a fully automated pipeline to train and predict highly reliable genes with GeneMark-ETP and AUGUSTUS. The result of the pipeline is the combined gene set of both gene prediction tools, which only contains genes with very high support from extrinsic evidence.

References:

Bruna, T., Hoff, K.J., Lomsadze, A., Stanke, M., & Borodovsky, M. BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database NAR Genomics and Bioinformatics 2021, 3(1):lqaa108, doi: 10.1093/nargab/lqaa108.
PubMed NAR Genomics and Bioinformatics, 2021

• braker GitHub Page

• Module Name: braker (see the modules page for more information)
• Unusual environment variables set
  • BRAKER_TEST_DATA sample data for running braker
  • BRAKER has to run some steps on a single thread, others can take advantage of multiple threads. But please do not set up more than 8 threads for BRAKER. Otherwise, the rest of threads will be idle.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive -c 8 --mem=4g --gres=lscratch:10 
[user@cn3144 ~]$ module load braker 
Loading braker  3

[user@cn3144 ]$ cp -r $BRAKER_TEST_DATA/*.fa . 

[user@cn3144 ]$ 
	braker.pl --genome=genome.fa --prot_seq=proteins.fa --threads $SLURM_CPUS_PER_TASK

Create a batch input file (e.g. braker.sh). For example:

#! /bin/bash

module load braker || exit 1
wget http://bioinf.uni-greifswald.de/augustus/datasets/RNAseq.bam
braker.pl --genome genome.fa --bam RNAseq.bam --threads $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch -c 8 --mem=10g braker.sh