SOAPsplice

SOAPsplice is a software tool that detects splice junctions using RNA-Seq data. RNA-Seq is a method that uses next-generation sequencing technologies to sequence the transcriptome, thereby facilitating genome-wide analysis of splice junction sites. The tool is designed to work without using any information on known splice junctions.

SOAPsplice uses a two-step approach to detect splice junctions. The tool identifies as many reasonable splice junction candidates as possible in the first step. After this, the second step involves filtering out false positives with two effective filtering strategies.

The tool has been demonstrated to detect many reliable splice junctions with low false positive rates in both simulated and real datasets. It is particularly effective when sequencing depth is low. Compared to other existing tools, SOAPsplice provides significant improvement in detecting splice junctions.