BRAKER is availabe from github at

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.

BRAKER1 required two input files:

  • genome file in fasta format,
  • corresponding RNA-Seq alignment file (must contain spliced alignments) in bam format.

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.

With the most recent release, BRAKER2, training of GeneMark-EP from alignment information of proteins from species with a longer evolutionary distance to the target genome is possible. You may thus achieve good gene prediction accuracy of GeneMark-EP and AUGUSTUS in the absence of RNA-Seq data. BRAKER1 functionality is fully maintained by BRAKER2. You find more information about BRAKER2 on our poster and in the slides from our talk at Plants and Animal Genomes conference 2018.


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:

Level Arabidopsis thaliana Caenorhabditis elegans Drosophila melanogaster S. pombe*
Gene Sens. 64.4 51.3 55.0 41.0 64.9 55.2 77.4 42.8 79.7
Gene Spec. 52.0 52.2 55.2 30.8 59.4 46.3 80.5 68.7 72.6
Exon Sens. 82.9 76.1 80.2 69.4 75.0 66.4 83.2 50.1 79.6
Exon Spec. 79.0 76.1 85.3 62.3 81.7 66.9 83.2 71.4 81.7
*) Schizosaccharomyces pombe


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

For usage with protein alignment data from remotely related species (result of the GeneMark-EP protein mapping pipeline):

perl --genome=genome.fa --hints=protein.gff --epmode

BRAKER2 produces three important output files in the working directory:

  • hintsfile.gff - The introns extraced from RNAseq.bam. These introns are used for training GeneMark-ET and for predicting genes with AUGUSTUS. The file is in gff format (see section 3, input argument --hints). If protein data is used, hintsfile.gff contains additional hint types generated from protein data. Those additional hints are used by AUGUSTUS, only.
  • genemark.gtf - Genes predicted by GeneMark-EX in gtf format
  • augustus.gff - Genes predicted by AUGUSTUS in gtf format


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: