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

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

Author information

1
Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

Abstract

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 http://odin.mdacc.tmc.edu/∼xsu1/VirusSeq.html.

CONTACT:

xsu1@mdanderson.org

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
23162058
PMCID:
PMC3546792
DOI:
10.1093/bioinformatics/bts665
[Indexed for MEDLINE]
Free PMC Article

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