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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 preprint can be found on bioRXiv

Please feel free to email us with comments and feedback or post them on the google group google group . This is a very new version of the software and we looking forward to ironing out bugs etc. with our pilot users. If you find that everything goes smoothly, we'd also like to know that!