JAFFA: High sensitivity transcriptome-focused fusion gene detection [article]

Nadia M Davidson, Ian J Majewski, Alicia Oshlack
2015 biorxiv/medrxiv   pre-print
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
more » ... riptome 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.
doi:10.1101/013698 fatcat:45mgleck4jcithyoj6nnig4vy4