Braker2
Description
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.
License
Free of charge for academic institutions.
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of braker2 and load default version of braker2 as
module avail braker2/ # list available modules module load braker2 # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail braker2
and choose explicit version you want to use.
For use on multiple cores try set --cores=$PBS_NUM_PPN parameter.
Documentation
https://github.com/Gaius-Augustus/BRAKER/blob/master/README.TXT
https://github.com/Gaius-Augustus/BRAKER/blob/master/docs/userguide.pdf