FusionFinder – automate the discovery of candidate gene fusion partners from RNA-Seq data

FusionFinder is Perl-based software designed to automate the discovery of candidate gene fusion partners from single-end (SE) or paired-end (PE) RNA-Seq read data. FusionFinder was applied to data from a previously published analysis of the K562 chronic myeloid leukaemia (CML) cell line. FusionFinder successfully replicated the findings of this study and detected additional previously unreported fusion genes in their dataset, which were confirmed experimentally. These included two isoforms of a fusion involving the genes BRK1 and VHL, whose co-deletion has previously been associated with the prevalence and severity of renal-cell carcinoma.

FusionFinder is made freely available for non-commercial use and can be downloaded from the project website (http://bioinformatics.childhealthresearc​h.org.au/software/fusionfinder/).

  • Francis RW, Thompson-Wicking K, Carter KW, Anderson D, Kees UR, Beesley AH. (2012) FusionFinder: A Software Tool to Identify Expressed Gene Fusion Candidates from RNA-Seq Data. PLoS One 7(6):e39987. [article]