Introduction

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

Publications

  1. STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.
    Cite this
    Karczewski KJ, Fernald GH, Martin AR, Snyder M, Tatonetti NP, Dudley JT, 2014-01-01 - PloS one

Credits

  1. Konrad J Karczewski
    Developer

    Biomedical Informatics Training Program, Stanford University School of Medicine, United States of America

  2. Guy Haskin Fernald
    Developer

    Biomedical Informatics Training Program, Stanford University School of Medicine, United States of America

  3. Alicia R Martin
    Developer

    Biomedical Informatics Training Program, Stanford University School of Medicine, United States of America

  4. Michael Snyder
    Developer

    Department of Genetics, Stanford University School of Medicine, United States of America

  5. Nicholas P Tatonetti
    Developer

    Department of Biomedical Informatics, Columbia University, United States of America

  6. Joel T Dudley
    Investigator

    Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, United States of America

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Summary
AccessionBT006805
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByJoel T Dudley