JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts then searches for gene fusions. This package contains the wrappers jaffa-direct, jaffa-assembly, and jaffa-hybrid. You can pass the “refSeq” parameter in the environment variables JAFFA_REF_BASE. Otherwise, pass any paramters to the wrappers as you would to the bpipe JAFFA_{method} call in the manual.

Home https://github.com/Oshlack/JAFFA
Versions 1.08, 1.09
License GPLv3
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/jaffa


With an activated Bioconda channel (see 2. Set up channels), install with:

conda install jaffa

and update with:

conda update jaffa


A Docker container is available at https://quay.io/repository/biocontainers/jaffa.