VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue
Y Chen, H Yao, EJ Thompson, NM Tannir… - …, 2013 - academic.oup.com
Y Chen, H Yao, EJ Thompson, NM Tannir, JN Weinstein, X Su
Bioinformatics, 2013•academic.oup.comWe 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 …
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 …
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.
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