Introduction

Accurate detection of viruses in plants and animals is critical for agriculture production and human health. Deep sequencing and assembly of virus-derived small interfering RNAs has proven to be a highly efficient approach for virus discovery. Here we present VirusDetect, a bioinformatics pipeline that can efficiently analyze large-scale small RNA (sRNA) datasets for both known and novel virus identification. VirusDetect performs both reference-guided assemblies through aligning sRNA sequences to a curated virus reference database and de novo assemblies of sRNA sequences with automated parameter optimization and the option of host sRNA subtraction. The assembled contigs are compared to a curated and classified reference virus database for known and novel virus identification, and evaluated for their sRNA size profiles to identify novel viruses. Extensive evaluations using plant and insect sRNA datasets suggest that VirusDetect is highly sensitive and efficient in identifying known and novel viruses. VirusDetect is freely available at http://bioinfo.bti.cornell.edu/tool/VirusDetect/.

Publications

  1. VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs.
    Cite this
    Zheng Y, Gao S, Padmanabhan C, Li R, Galvez M, Gutierrez D, Fuentes S, Ling KS, Kreuze J, Fei Z, 2017-01-01 - Virology

Credits

  1. Yi Zheng
    Developer

    Boyce Thompson Institute, Ithaca, United States of America

  2. Shan Gao
    Developer

    Boyce Thompson Institute, Ithaca, United States of America

  3. Chellappan Padmanabhan
    Developer

    U.S. Vegetable Laboratory, U.S. Department of Agriculture-Agricultural Research Service, United States of America

  4. Rugang Li
    Developer

    U.S. Vegetable Laboratory, U.S. Department of Agriculture-Agricultural Research Service, United States of America

  5. Marco Galvez
    Developer

    Virology laboratory, International Potato Center (CIP), Peru

  6. Dina Gutierrez
    Developer

    Virology laboratory, International Potato Center (CIP), Peru

  7. Segundo Fuentes
    Developer

    Virology laboratory, International Potato Center (CIP), Peru

  8. Kai-Shu Ling
    Developer

    U.S. Vegetable Laboratory, U.S. Department of Agriculture-Agricultural Research Service, United States of America

  9. Jan Kreuze
    Developer

    Virology laboratory, International Potato Center (CIP), Peru

  10. Zhangjun Fei
    Investigator

    Boyce Thompson Institute, Ithaca, United States of America

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Summary
AccessionBT001373
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByZhangjun Fei