Framework of SOAPfuse for discovering fusion events. (a) Model of the fusion event from Gene A and Gene B that is supported by span-reads and junc-reads. Gene A and reads mapped to it are in blue, and Gene B is in orange. The junction site is marked by a yellow dot. Two span-reads and two junc-reads are shown. (b) The four parts of the SOAPfuse algorithm: read alignment against the human genome reference and annotated transcript sequences; identifying candidate gene pairs by seeking span-reads; detection of predicted fusions; filtering fusions with several criteria to generate the final high-confidence fusion transcript list. Methods with central roles in the algorithm are indicated in red. Steps marked by an asterisk indicate key filtering steps.