ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution

Bioinformatics. 2013 Mar 1;29(5):649-51. doi: 10.1093/bioinformatics/btt011. Epub 2013 Jan 12.


Summary: 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.

Availability: VFS is distributed under GPL version 3 at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Gene Fusion*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • RNA / chemistry*
  • Sequence Analysis, DNA
  • Sequence Analysis, RNA
  • Software*
  • Virus Integration*


  • RNA