SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data

Genome Biol. 2013 Feb 14;14(2):R12. doi: 10.1186/gb-2013-14-2-r12.


We have developed a new method, SOAPfuse, to identify fusion transcripts from paired-end RNA-Seq data. SOAPfuse applies an improved partial exhaustion algorithm to construct a library of fusion junction sequences, which can be used to efficiently identify fusion events, and employs a series of filters to nominate high-confidence fusion transcripts. Compared with other released tools, SOAPfuse achieves higher detection efficiency and consumed less computing resources. We applied SOAPfuse to RNA-Seq data from two bladder cancer cell lines, and confirmed 15 fusion transcripts, including several novel events common to both cell lines. SOAPfuse is available at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Cell Line, Tumor
  • Gene Fusion*
  • Humans
  • RNA, Messenger / genetics*
  • Sensitivity and Specificity
  • Sequence Alignment / methods*
  • Sequence Analysis, RNA / methods*


  • RNA, Messenger