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STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud

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  • Konrad J Karczewski
  • Guy Haskin Fernald
  • Alicia R Martin
  • Michael Snyder
  • Nicholas P Tatonetti
  • Joel T Dudley

Abstract

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.

Suggested Citation

  • Konrad J Karczewski & Guy Haskin Fernald & Alicia R Martin & Michael Snyder & Nicholas P Tatonetti & Joel T Dudley, 2014. "STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-4, January.
    • Handle: RePEc:plo:pone00:0084860
    DOI: 10.1371/journal.pone.0084860
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