@article {Davidson013698, author = {Nadia M. Davidson and Ian J. Majewski and Alicia Oshalck}, title = {JAFFA: High sensitivity transcriptome-focused fusion gene detection}, elocation-id = {013698}, year = {2015}, doi = {10.1101/013698}, publisher = {Cold Spring Harbor Laboratory}, 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 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.}, URL = {https://www.biorxiv.org/content/early/2015/01/12/013698}, eprint = {https://www.biorxiv.org/content/early/2015/01/12/013698.full.pdf}, journal = {bioRxiv} }