Introduction

SpeedSeq is an open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement. SpeedSeq offers performance competitive with or superior to current methods for detecting germline and somatic single-nucleotide variants, structural variants, insertions and deletions, and it includes novel functionality for streamlined interpretation.

Publications

  1. SpeedSeq: ultra-fast personal genome analysis and interpretation.
    Cite this
    Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM, 2015-10-01 - Nature methods

Credits

  1. Colby Chiang
    Developer

    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, United States of America

  2. Ryan M Layer
    Developer

    Utah Science Technology and Research (USTAR) Center for Genetic Discovery, University of Utah School of Medicine, United States of America

  3. Gregory G Faust
    Developer

    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, United States of America

  4. Michael R Lindberg
    Developer

    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, United States of America

  5. David B Rose
    Developer

    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, United States of America

  6. Erik P Garrison
    Developer

    Wellcome Trust Sanger Institute, Hinxton, Germany

  7. Gabor T Marth
    Developer

    Utah Science Technology and Research (USTAR) Center for Genetic Discovery, University of Utah School of Medicine, United States of America

  8. Aaron R Quinlan
    Developer

    Utah Science Technology and Research (USTAR) Center for Genetic Discovery, University of Utah School of Medicine, United States of America

  9. Ira M Hall
    Investigator

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

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Summary
AccessionBT006950
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByIra M Hall