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. SOAPfusion is accurate and efficient for fusion discovery with high sensitivity (≥93%), low false-positive rate (≤1.36%), even the coverage is as low as 10×, highlighting its ability to detect fusions efficiently at low sequencing cost. From real data of Universal Human Reference RNA (UHRR) samples, SOAPfusion detected 7 novel fusion genes, more than other existing tools and all genes have been validated through reverse transcription-polymerase chain reaction followed by Sanger sequencing. SOAPfusion thus proves to be an effective method with precise applicability in search of fusion transcripts, which is advantageous to accelerate pathological and therapeutic cancer studies.

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. In both simulated and real datasets, SOAPsplice is able to detect many reliable splice junctions with low false positive rate. The improvement gained by SOAPsplice, when compared to other existing tools, becomes more obvious when the depth of sequencing is low. SOAPsplice is freely available at http://soap.genomics.org.cn/soapsplice.html.