title: ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.
abstract: CONCLUSIONS
  Insertional mutagenesis from virus infection is an important pathogenic risk for the development of cancer. Despite the advent of high-throughput sequencing, discovery of viral integration sites and expressed viral fusion events are still limited. Here, we present ViralFusionSeq (VFS), which combines soft-clipping information, read-pair analysis and targeted de novo assembly to discover and annotate viral-human fusions. VFS was used in an RNA-Seq experiment, simulated DNA-Seq experiment and re-analysis of published DNA-Seq datasets. Our experiments demonstrated that VFS is both sensitive and highly accurate.
  
  
  BACKGROUND
  VFS is distributed under GPL version 3 at http://hkbic.cuhk.edu.hk/software/viralfusionseq
authors: School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.
authors: Jing-Woei
authors: JW
authors: Li
authors: Raymond
authors: R
authors: Wan
authors: Chi-Shing
authors: CS
authors: Yu
authors: Ngai Na
authors: NN
authors: Co
authors: Nathalie
authors: N
authors: Wong
authors: Ting-Fung
authors: TF
authors: Chan
mesh_terms: D045744:Cell Line, Tumor; D050939:Gene Fusion; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D012313:RNA / Q000737:chemistry*; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D012984:Software; D016662:Virus Integration
chemical_list: D012313:RNA