deFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. A classifier trained on real fusions and false positives is applied to the assembled sequences. The software produces a fully annotated output for each predicted fusion. The software is designed to be run out of the box with little configuration, and is compatible SGE, PBS and LSF compute clusters.
deFuse has been used to discover gene fusions in tumour samples for the following papers:
MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers, Nature 2011
The deFuse algorithm and results from an application to ovarian tumours and sarcomas was published in PLoS Computational Biology:
deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data
Please see the sourceforge page, http://defuse.sf.net for more details.
Feel free to email the author if you have any questions or issues.