Dataset Information
VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue.
Ontology highlight
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.orgSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Chen Y
PROVIDER: S-EPMC3546792 | biostudies-literature | 2013 Jan
REPOSITORIES: biostudies-literature
Publications
VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue.
Bioinformatics (Oxford, England) 20121117 2
<h4>Summary</h4>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 ...[more]
