BREW3R stands for Bulk RNA-seq Evidence-based Workflow for 3' UTR Reannotation.
This workflow enables extending an existing gtf downloaded on a public website, like Ensembl, Genecode or UCSC, using de novo gene annotation with StringTie on full length bulk RNA-seq.
BREW3R highly relies on a R package called BREW3R.r available on bioconductor.
Here is a schema of the workflow:
All dependencies of BREW3R have been installed into a docker container.
If you want to run BREW3R, you can use Galaxy or the sbatch scripts available in the slurm directory.