Introduction

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.VirusSeq has been implemented in PERL and is available at http://odin.mdacc.tmc.edu/∼xsu1/VirusSeq.html.xsu1@mdanderson.orgSupplementary data are available at Bioinformatics online.

Publications

  1. VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue.
    Cite this
    Chen Y, Yao H, Thompson EJ, Tannir NM, Weinstein JN, Su X, 2013-01-01 - Bioinformatics (Oxford, England)

Credits

  1. Yunxin Chen
    Developer

    Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, United States of America

  2. Hui Yao
    Developer

  3. Erika J Thompson
    Developer

  4. Nizar M Tannir
    Developer

  5. John N Weinstein
    Developer

  6. Xiaoping Su
    Investigator

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT004093
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByXiaoping Su