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JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions. It will output the names and locations of candidate gene fusions along with the cDNA sequence of their breakpoints. JAFFA is based on the idea of comparing a transcriptome (e.g. in a cancer sample) against a reference transcriptome. In this way, it is a transcript-centric approach rather than a genome-centric approach like other fusion finders. In validation studies, JAFFA performed well over a range of read lengths - from 50bp to full-length transcripts and on single and paired-end reads. For more information please see one of the wiki pages below:

• Download JAFFA
• Check out HowToSetUpJAFFA for installation and basic running instructions.
• See our full example
• Get details about the output of JAFFA
• Our paper, JAFFA: High sensitivity transcriptome-focused fusion gene detection, just came out at Genome Medicine! (May 11th 2015)
• JAFFA 2.0 now released (Nov. 2020) which calls fusions in long reads such as ONT and runs significantly faster for short reads.
• JAFFAL: detecting fusion genes with long-read transcriptome sequencing (Jan 2022) - our new paper on long read fusion finding.

Please feel free to email us with comments and feedback or post them on the google group. We are always happy to get feedback about our software, whether it's good or bad.

JAFFA is available under the GPL open source license and contributions to the software are welcome.