SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads.

Motivation: RNA-Seq provides a powerful approach to carry out ab initio investigation of fusion transcripts representing critical translocation and post-transcriptional events that recode hereditary information. Most of the existing computational fusion detection tools are challenged by the issues of accuracy and how to handle multiple mappings.

Results: We present a novel tool SOAPfusion for fusion discovery with paired-end RNA-Seq reads.

SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data.

RNA-Seq, a method using next generation sequencing technologies to sequence the transcriptome, facilitates genome-wide analysis of splice junction sites. In this paper, we introduce SOAPsplice, a robust tool to detect splice junctions using RNA-Seq data without using any information of known splice junctions. SOAPsplice uses a novel two-step approach consisting of first identifying as many reasonable splice junction candidates as possible, and then, filtering the false positives with two effective filtering strategies.