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BRAKER specifications


Unique identifier OMICS_10582
Alternative name BRAKER1
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data BRAKER requires two input files: an RNA-seq alignment file in bam format and a corresponding genome file in fasta format.
Operating system Unix/Linux
Programming languages Perl
License Artistic License version 2.0
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes




No version available


  • person_outline Mark Borodovsky

Publication for BRAKER

BRAKER citations


Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen fixing rhizobium symbioses

Proc Natl Acad Sci U S A
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115
call_split See protocol

[…] r tracks were used: (i) SNAP () trained on P. andersonii transdecoder transcript annotations; (ii) SNAP trained on T. orientalis transdecoder transcript annotations; (iii) Augustus (), as used in the BRAKER pipeline, trained on RNA-seq alignments (); and (iv) GeneMark-ET, as used in the BRAKER pipeline, trained on RNA-seq alignments ().First, all evidence tracks were processed by Maker-P (). The r […]


Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species

PLoS Biol
PMCID: 5916493
PMID: 29689044
DOI: 10.1371/journal.pbio.2004830

[…] -species ‘rotifera’) and compared to each assembly using RepeatMasker v4.0.7 []. Low-complexity regions and simple repeats were additionally soft-masked.Gene prediction was then performed using BRAKER v1.9 [] where RNASeq data was available (A. ricciae and R. magnacalcarata). Briefly, RNASeq reads were aligned to the masked assembly using STAR, specifying the ‘twoPassMode Basic’ parameter to […]


Ginseng Genome Database: an open access platform for genomics of Panax ginseng

BMC Plant Biol
PMCID: 5898050
PMID: 29649979
DOI: 10.1186/s12870-018-1282-9

[…] ize. The repeat sequences were identified and masked using RepeatModeler [] and RepeatMasker []. An automatic gene prediction was performed using evidence modeler (EVM) [] with ab initio predictions (BRAKER 1 []), protein evidence, ESTs and RNA-Seq evidence []. After the removal of the transposon sequences, a total 59,352 putative protein coding genes were predicted. These genes were functionally […]


Nucleus specific expression in the multinuclear mushroom forming fungus Agaricus bisporus reveals different nuclear regulatory programs

Proc Natl Acad Sci U S A
PMCID: 5924919
PMID: 29643074
DOI: 10.1073/pnas.1721381115
call_split See protocol

[…] The P1 and P2 genomes () were annotated with BRAKER1 () and AUGUSTUS 3.0.2 () using the pooled RNA-seq data from the mushroom tissue dataset (SI Appendix O). Named genes are provided in SI Appendix P. Functional annotations are provided in SI Ap […]


A Whole Genome Assembly of the Horn Fly, Haematobia irritans, and Prediction of Genes with Roles in Metabolism and Sex Determination

PMCID: 5940159
PMID: 29602812
DOI: 10.1534/g3.118.200154

[…] is available. This 44,357 bp partial transcript isoform (LOC_Hi_v1_g8496.t1) contains 3 exons from the sodium channel protein coding region and lacks a stop codon according to the prediction made by BRAKER1. Our previous research had identified at least four introns in this region of the sodium channel gene and the genomic sequence from this locus will assist our investigations into possible alte […]


Improving the annotation of the Heterorhabditis bacteriophora genome

PMCID: 5906903
PMID: 29617768
DOI: 10.1093/gigascience/giy034

[…] Interproscan v5.19–58.0 (Interproscan, RRID:SCR_005829) [] was used in protein mode to identify matches in the BRAKER1 and published proteomes in the following databases: TIGRFAM v15.0, ProDom v2006.1, SMART-7.1, SignalP-EUK v4.1, PrositePatterns v20.119, PRINTS v42.0, SuperFamily v1.75, Pfam v29.0, and Prosit […]


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BRAKER institution(s)
Ernst Moritz Arndt Universität Greifswald, Institute for Mathematics and Computer Science, Greifswald, Germany
BRAKER funding source(s)
This work is supported in part by the US National Institutes of Health grant HG000783.

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