BRAKER statistics

info info

Citations per year


Popular tool citations

chevron_left Gene prediction chevron_right

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?


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

[…] 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 (). […]


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

[…] a vegetative mycelium sample. the compost dataset exhibited high amounts of pcr duplicates (si appendix n), which we removed using fastuniq ()., 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 […]


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

[…] p. repeatmasker open-4.0 2008–2015, using d. melanogaster as reference species, resulting in approximately 3.2% (supplementary table s1) of the genome being masked. braker1 () was used for gene prediction which uses genemark-et () to generate initial ab initio gene predictions and further trains augustus () to produce a final set of gene models. although braker1 […]


Improving the annotation of the Heterorhabditis bacteriophora genome

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

[…] pipeline to identify potential contaminants. while present (0.2% of the genome span, 0.4% of predicted proteins), assembly contamination was not significant., re-prediction of the gene set using braker1 and published transcriptome data generated a predicted proteome that was very different from the published one. the new gene set had a much reduced complement of unique proteins, better […]


Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

Environ Microbiol
PMCID: 5900883
PMID: 29327410
DOI: 10.1111/1462-2920.14043

[…] table s6). the norz gene has been found to date in both denitrifiers and non‐denitrifying strains, suggesting a function in detoxifying nitric oxide (cramm et al., ; büsch et al., ; leang et al., ; braker and tiedje, ; philippot, ) rather than in denitrification. taken together, anaerobic respiration with either nitrate, nitrite, nitric oxide or nitrous oxide as alternative electron acceptors […]


A Near Complete Haplotype Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity

PMCID: 5821087
PMID: 29463659
DOI: 10.1128/mBio.02275-17

[…] at our study’s github respository., we annotated genes on primary contigs and haplotigs independently. we combined rna-seq-guided ab initio predictions by using codingquarry v2.0 () and braker v1.9 () with de novo transcriptome assembly approaches of trinity v2.2.0 () and pasa v2.0.1 (). gene models were unified using evidencemodeler v1.1.1 () and the weights reported in file 16., […]

Want to access the full list of citations?
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.

BRAKER reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review BRAKER