Bellerophontes – a fully automated framework for the detection of novel fusion transcripts in paired end RNA-Seq data

Bellerophontes is a new framework for the detection of fusion transcripts through short paired-end reads which integrates splicing-driven alignment and abundance estimation analysis, producing a more accurate set of reads supporting the junction discovery and taking into account also not annotated transcripts. Bellerophontes performs a selection of putative junctions on the basis of a match to an accurate gene fusion model. Bellerophontes runs on top of TopHat and Cufflinks tools (developed by Trapnell et al.). The analysis is based on the results of TopHat alignment and Cufflinks transcript isoform detection.

AVAILABILITY:  Bellerophontes JAVA/Perl/Bash software implementation is free and available at

  • Abate F, Acquaviva A, Paciello G, Ficarra E, Ferrarini A, Delledonne M, Soverini S, Martinelli G, Macii E. (2102) Bellerophontes: A RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model. Bioinformatics [Epub ahead of print]. [abstract]