title: JAFFA: High sensitivity transcriptome-focused fusion gene detection.
abstract: 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 optimised for short reads. JAFFA (https://github.com/Oshlack/JAFFA/wiki) is a sensitive fusion detection method that outperforms other methods with reads of 100 bp 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.
authors.affiliation: Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052 Australia.
authors.forename: Nadia M
authors.initials: NM
authors.lastname: Davidson
authors.affiliation: Division of Cancer and Haematology, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria 3052 Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010 Australia.
authors.forename: Ian J
authors.initials: IJ
authors.lastname: Majewski
authors.affiliation: Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052 Australia ; Department of Genetics, The University of Melbourne, Parkville, Victoria 3010 Australia.
authors.forename: Alicia
authors.initials: A
authors.lastname: Oshlack