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Genomic instability is a hallmark of cancer and, as such, structural alterations and fusion genes are common events in the cancer landscape. RNA sequencing (RNA-Seq) is a powerful method for profiling cancers, but current methods for identifying fusion genes are optimized for short reads. JAFFA (https://code.google.com/p/jaffa-project/) is a sensitive fusion detection method that clearly out-performs other methods with reads of 100bp or greater. JAFFA compares a cancer transcriptome to thedoi:10.1101/013698 fatcat:45mgleck4jcithyoj6nnig4vy4