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BRAKER is a tool for fully automated genome annotation with GeneMark-ET and AUGUSTUS. BRAKER is a joint project of Georgia Institute of Technology, USA and Institute for Mathematics and Computer Science, University of Greifswald, Germany.

In its initial version, BRAKER1 was able to process genome and RNA-Seq data, only. BioTechniques reported on BRAKER1 on 02/05/2016.

BRAKER1 required two input files:

First, GeneMark-ET performs RNA-Seq supported iterative training and generates initial gene structures. Second, AUGUSTUS uses predicted genes for training and then integrates RNA-Seq read information as extrinsic evidence into final gene predictions.

The most recent release, BRAKER2, in addition takes a protein sequence file, generates protein to genome alignments with GenomeThreader, Exonerate or Spaln, and incorporates protein alignment information into the gene prediction step with AUGUSTUS. BRAKER1 functionality is fully maintained by BRAKER2.


We compare prediction accuracy of BRAKER1 on four model species genomes to accuracy of MAKER2 and CodingQuarry (only applicable to fungi). The following table is an excerpt from our publication BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS, Table1:

LevelArabidopsis thaliana Caenorhabditis elegans Drosophila melanogaster Schizosaccharomyces pombe
Gene Sens.64.451.355.041.064.955.277.442.879.7
Gene Spec.
Exon Sens.82.976.180.269.475.066.483.250.179.6
Exon Spec.


Download BRAKER2 from The most recent release is version 2.0, November 9th 2017. Example data for testing the BRAKER2 pipeline is available at (1.1 GB).


For straight forward gene prediction in a genome file with a RNA-Seq alignment bam file, run the following command:

perl --genome=genome.fa --bam=RNAseq.bam

For usage with protein data, choose one aligner out of GenomeThreader (gth), Exonerate (exonerate) and Spaln (spaln):

perl --genome=genome.fa --bam=RNAseq.bam --prot_seq=protein.fa --prg=(gth|exonerate|spaln) --ALIGNMENT_TOOL_PATH=/path/to/aligner

BRAKER2 produces three important output files in the working directory:


We have to correct one important reference in the BRAKER1 publication. In computations of the gene prediction accuracy for the D. melanogaster genome we used the r6.07 version of the fly genome and annotation. However, the Supplementary materials to the paper (available at the "Bioinformatics" journal website) incorrectly cite the earlier r5.55 version of the D. melanogaster genome.


Please cite the following publications when using BRAKER for your project:

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