Experiences building Globus Genomics: a next‐generation sequencing analysis service using Galaxy, Globus, and Amazon Web Services
Open accessAbstract
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.
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References 29 · Cited by 73
- Authors
- Madduri, R. K., Sulakhe, D., Lacinski, L., Liu, B., Rodriguez, A., Chard, K., Dave, U. J., & Foster, I. T.
- Affiliations
- Argonne National Laboratory (US)
- Computation Institute University of Chicago and Argonne National Laboratory Chicago IL USA
- Corresponding author
- Madduri, Ravi K.
- Venue
- Concurrency and Computation: Practice and Experience
- Publisher
- Wiley
- Published
- 2014-04-08
- Volume
- 26
- Issue
- 13
- Pages
- 2266-2279
- ISSN
- 1532-0626 (ISSN-L)
- 1532-0634
- PMC
- PMC4203657
- OpenAlex
- W1721251433
- Cited by
- 73
- References
- 29
- Citations by year
- 2024: 1 · 2023: 1 · 2022: 2 · 2021: 13 · 2020: 7 · 2019: 6 · 2018: 10 · 2017: 10 · 2016: 9 · 2015: 7 · 2014: 7
- FWCI
- 20.54
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Concurrency and Computation Practice and Experience (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Cardiovascular Research Grid (R24HL085343)
- US Department of Energy (DE-AC02-06CH11357)
- Topics
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Physical Sciences › Computer Science › Information Systems › Cloud Computing and Resource Management
- Physical Sciences › Computer Science › Computer Networks and Communications › Distributed and Parallel Computing Systems
- Keywords
- next-generation sequencing data analysis, Amazon EC2, automated bioinformatics pipeline, cloud computing, on-demand resource provisioning, genomic data processing
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