RT Journal Article SR Electronic T1 JAFFA: High sensitivity transcriptome-focused fusion gene detection JF bioRxiv FD Cold Spring Harbor Laboratory SP 013698 DO 10.1101/013698 A1 Nadia M. Davidson A1 Ian J. Majewski A1 Alicia Oshlack YR 2015 UL http://biorxiv.org/content/early/2015/01/23/013698.abstract AB 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 the reference transcriptome, rather than the genome, where the cancer transcriptome is inferred using long reads directly or by de novo assembling short reads.