title: SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads.
abstract: BACKGROUND
  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.
authors.affiliation: Department of Computer Science, The University of Hong Kong, Hong Kong, China, BGI-Shenzhen, Shenzhen, China, Department of Biology, University of Copenhagen, Copenhagen, Denmark, King Abdulaziz University, Jeddah, Saudi Arabia, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen and Guangzhou Key Laboratory of Cancer Trans-Omics Research, BGI-Guangzhou, Guangzhou, China.
authors.forename: Jikun
authors.initials: J
authors.lastname: Wu
authors.forename: Wenqian
authors.initials: W
authors.lastname: Zhang
authors.forename: Songbo
authors.initials: S
authors.lastname: Huang
authors.forename: Zengquan
authors.initials: Z
authors.lastname: He
authors.forename: Yanbing
authors.initials: Y
authors.lastname: Cheng
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Tak-Wah
authors.initials: TW
authors.lastname: Lam
authors.forename: Zhiyu
authors.initials: Z
authors.lastname: Peng
authors.forename: Siu-Ming
authors.initials: SM
authors.lastname: Yiu
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology; D050939:Gene Fusion; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008969:Molecular Sequence Data; D009369:Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods; D012689:Sequence Homology, Nucleic Acid; D012984:Software