Bellerophontes is a fully automated framework for the detection of novel fusion transcripts in paired end RNA-Seq data. It detects putative fusion genes by searching those reads that discordantly match on different genes. Then, the tool applies several modular filters in order to select those fused genes matching an accurate gene fusion model based on experimental evidences reported in recent literature. Bellerophontes runs on top of TopHat and Cufflinks tools. The analysis is based on the results of TopHat alignment and Cufflinks transcript isoform detection.