FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data

Andrea Sboner, Lukas Habegger, Dorothee Pflueger, Stephane Terry, David Z. Chen, Joel S. Rozowsky, Ashutosh K. Tewari, Naoki Kitabayashi, Benjamin J. Moss, Mark S. Chee, Francesca Demichelis, Mark A. Rubin, Mark B. Gerstein
Genome Biology 21 Oct. 2010; 11:R104 - doi:10.1186/gb-2010-11-10-r104

FusionSeq is a computational framework to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts such as misalignments or random pairing of transcript fragments and it ranks candidates according to several statistics. It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including 8 cancers with and without known rearrangements.

Documentation for the user

This section provides the documentation for the user, including instructions to download and install the source code.

Documentation for the developer

This section provides more specific documentation for the developer.


Here you can download the software. Please read the documentation first.

Example workflow

Here is an example on how to run FusionSeq.


Some figures about FusionSeq.


Some examples of the web-interface. Use the sample IDs in the manuscript to access the results, e.g. 106_T, 1700_D, etc.


Papers citing FusionSeq.



last update: 01-Nov-2010