VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue

Bioinformatics. 2013 Jan 15;29(2):266-7. doi: 10.1093/bioinformatics/bts665. Epub 2012 Nov 17.


Summary: We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on whole-transcriptome sequencing (RNA-Seq) data of 256 human cancer samples from The Cancer Genome Atlas. Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole-genome sequencing data of human tissue.

Availability: VirusSeq has been implemented in PERL and is available at∼xsu1/VirusSeq.html.


Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Genome, Human
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Neoplasms / genetics
  • Neoplasms / virology*
  • Sequence Analysis, RNA
  • Software*
  • Virus Integration*
  • Viruses / genetics
  • Viruses / isolation & purification*