Experiences building Globus Genomics: a next‐generation sequencing analysis service using Galaxy, Globus, and Amazon Web Services | Zendy

Madduri Ravi K. | Zendy; Sulakhe Dinanath | Zendy; Lacinski Lukasz | Zendy; Liu Bo | Zendy; Rodriguez Alex | Zendy; Chard Kyle | Zendy; Dave Utpal J. | Zendy; Foster Ian T. | Zendy

Premium

Experiences building Globus Genomics: a next‐generation sequencing analysis service using Galaxy, Globus, and Amazon Web Services

Author(s) -

Madduri Ravi K.,

Sulakhe Dinanath,

Lacinski Lukasz,

Liu Bo,

Rodriguez Alex,

Chard Kyle,

Dave Utpal J.,

Foster Ian T.

Publication year - 2014

Publication title -

concurrency and computation: practice and experience

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.309

H-Index - 67

eISSN - 1532-0634

pISSN - 1532-0626

DOI - 10.1002/cpe.3274

Subject(s) - computer science , workflow , pipeline transport , scheduling (production processes) , software , automation , reuse , service (business) , distributed computing , operating system , database , engineering , mechanical engineering , operations management , economy , environmental engineering , waste management , economics

SUMMARY We describe Globus Genomics, a system that we have developed for rapid analysis of large quantities of next‐generation sequencing genomic data. This system achieves a high degree of end‐to‐end automation that encompasses every stage of data analysis including initial data retrieval from remote sequencing centers or storage (via the Globus file transfer system); specification, configuration, and reuse of multistep processing pipelines (via the Galaxy workflow system); creation of custom Amazon Machine Images and on‐demand resource acquisition via a specialized elastic provisioner (on Amazon EC2); and efficient scheduling of these pipelines over many processors (via the HTCondor scheduler). The system allows biomedical researchers to perform rapid analysis of large next‐generation sequencing datasets in a fully automated manner, without software installation or a need for any local computing infrastructure. We report performance and cost results for some representative workloads. Copyright © 2014 John Wiley & Sons, Ltd.

This content is not available in your region!

Continue researching here.

Having issues? You can contact us here

Accelerating Research