FusionCatcher is an RNA-seq gene fusions finder pipeline has been released and made publicly available under GPL v3 license.
FusionCatcher has been used previously for finding fusion genes in these articles:
- S. Kangaspeska, et al., Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms, PLOS One, Oct. 2012. http://dx.plos.org/10.1371/journal.pone.0048745
- H. Edgren, et al., Identification of fusion genes in breast cancer by paired-end RNA-sequencing, Genome Biology, Vol. 12, Jan. 2011. http://genomebiology.com/2011/12/1/R6
More info about it can be found here: http://code.google.com/p/fusioncatcher/