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The rapidly growing number of sequenced genomes requires fully automated methods for accurate gene structure annotation. With this goal in mind, we have developed BRAKER1 [Hoff et al., 2015], a combination of GeneMark-ET [Lomsadze et al., 2014] and AUGUSTUS [Stanke et al., 2008, Stanke et al., 2006], that uses genomic and RNA-Seq data to automatically generate full gene structure annotations in novel genomes.

However, the quality of RNA-Seq data that is available for annotating a novel genome is variable, and in some cases, RNA-Seq data is not available, at all. BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-EX [Lomsadze et al., 2005, Ter-Hovhannisyan et al., 2008, Lomsadze et al., 2014] and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.

In contrast to other available methods that rely on protein homology information, BRAKER2 reaches high gene prediction accuracy even in the absence of the annotation of very closely related species and in the absence of RNA-Seq data. BRAKER2 can also combine RNA-Seq and protein homology information.


Available modules:



Free of charge for academic institutions.


module add braker2-20180831 --help

For use on multiple cores try set --cores=$PBS_NUM_PPN parameter.

See also other Use sections of programs used by Braker2: Augustus, GeneMark, Bamtools, SAMtools, GenomeThreader and Blast+. You may need to adjust Augustus config path to use BRAKER2 tool correctly.



Program manager