BRAKER3

BRAKER3 is a mixture of GeneMark-ET and AUGUSTUS that utilizes genomic and RNA-seq data to automatically generate full gene structure annotations in a novel genome. It is the latest of the BRAKER series that also utilizes RNA-seq data as well as protein data.

For input BRAKER3 expects genomic sequences that have been softmasked for Repeats. It cannot process the file otherwise. The example provided if for genomes of species for which RNA-Seq libraries with good transcriptome coverage are available and for which protein data is not at hand.

To load BRAKER3 on Palmetto 2 run the following:

module load biocontainers
module load braker3

After you have loaded it you can run the analysis as such:

braker.pl --species=yourSpecies --genome=genome.fasta --rnaseq_sets_ids=SRA_ID1,SRA_ID2

Parallel Capabilities: Multithreaded by default.