BRAKER protocols

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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



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  • person_outline Mark Borodovsky <>

Publication for BRAKER

BRAKER in pipelines

PMCID: 5765654
PMID: 29325559
DOI: 10.1186/s12915-017-0457-4

[…] for more details on the snp calling, map construction, and assembly validation procedure., to accurately predict the gene space of each newly assembled genome, we used the gene prediction software braker v1.9 []. braker combines coding sequence and intron hints based on the mapping of conserved protein sequences and introns identified in rna-seq data, respectively. we used rna-seq datasets […]

PMCID: 5815587
PMID: 29451893
DOI: 10.1371/journal.pone.0191824

[…] (3.37 mb) of the assembly. busco was used to assess gene space, identifying that 3689 of 3725 (99%) core sordariomycete genes were present in the assembly. gene prediction was carried out using braker1 and codingquary, which predicted a total of 10486 genes in the unmasked assembly., de novo assembly of the four illumina-only genomes resulted in assemblies of a similar size (32.4–32.9 mb) […]

PMCID: 5924919
PMID: 29643074
DOI: 10.1073/pnas.1721381115

[…] 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 […]

PMCID: 5624889
PMID: 28970504
DOI: 10.1038/s41598-017-12863-w

[…] genes in o. camponoti-rufipedis, we chose an approach that used them indirectly. augustus version 3.0.2 was used to predict genes, using the rna-seq-informed parameter files previously generated by braker1 version 1.1.8. for o. kimflemingiae sc16a (described above)., we functionally annotated the predicted proteins of all ophiocordyceps strains in this study. pfam version 27 was used to predict […]

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BRAKER in publications

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 (). […]

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 […]

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 […]

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 […]

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., […]

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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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