Introduction

The advent of Next Generation Sequencing (NGS) has vastly increased our ability to discover novel viruses and to systematically define the spectrum of viruses present in a given specimen. Such studies have led to the discovery of novel viral pathogens as well as broader associations of the virome with diverse diseases including inflammatory bowel disease, severe acute malnutrition and HIV/AIDS. Critical to the success of these efforts are robust bioinformatic pipelines for rapid classification of microbial sequences. Existing computational tools are typically focused on either eukaryotic virus discovery or virome composition analysis but not both. Here we present VirusSeeker, a BLAST-based NGS data analysis pipeline designed for both purposes. VirusSeeker has been successfully applied in several previously published virome studies. Here we demonstrate the functionality of VirusSeeker in both novel virus discovery and virome composition analysis.

Publications

  1. VirusSeeker, a computational pipeline for virus discovery and virome composition analysis.
    Cite this
    Zhao G, Wu G, Lim ES, Droit L, Krishnamurthy S, Barouch DH, Virgin HW, Wang D, 2017-03-01 - Virology

Credits

  1. Guoyan Zhao
    Developer

    Departments of Pathology & Immunology, Washington University School of Medicine, United States of America

  2. Guang Wu
    Developer

    Department of Molecular Microbiology, Washington University School of Medicine, United States of America

  3. Efrem S Lim
    Developer

    Department of Molecular Microbiology, Washington University School of Medicine, United States of America

  4. Lindsay Droit
    Developer

    Departments of Pathology & Immunology, Washington University School of Medicine, United States of America

  5. Siddharth Krishnamurthy
    Developer

    Department of Molecular Microbiology, Washington University School of Medicine, United States of America

  6. Dan H Barouch
    Developer

    Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, United States of America

  7. Herbert W Virgin
    Developer

    Departments of Pathology & Immunology, Washington University School of Medicine, United States of America

  8. David Wang
    Investigator

    Departments of Pathology & Immunology, Washington University School of Medicine, United States of America

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Summary
AccessionBT000647
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByDavid Wang