Genomics in the Cloud: Using Docker, GATK, and WDL in Terra
Language: English
Published by O'Reilly Media, 2020
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- New
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- Title
- Genomics in the Cloud: Using Docker, GATK, and WDL in Terra
- Author
- Auwera, Geraldine A. Van der
- Publisher
- O'Reilly Media
- Publication year
- 2020
- Condition
- new
- Binding
- Paperback
- Language
- English
- ISBN 10
- 1491975199
- ISBN 13
- 9781491975190
Data in the genomics field is booming. In just a few years, organizations such as the National Institutes of Health (NIH) will host 50+ petabytes—or over 50 million gigabytes—of genomic data, and they’re turning to cloud infrastructure to make that data available to the research community. How do you adapt analysis tools and protocols to access and analyze that volume of data in the cloud?
With this practical book, researchers will learn how to work with genomics algorithms using open source tools including the Genome Analysis Toolkit (GATK), Docker, WDL, and Terra. Geraldine Van der Auwera, longtime custodian of the GATK user community, and Brian O’Connor of the UC Santa Cruz Genomics Institute, guide you through the process. You’ll learn by working with real data and genomics algorithms from the field.
This book covers:
- Essential genomics and computing technology background
- Basic cloud computing operations
- Getting started with GATK, plus three major GATK Best Practices pipelines
- Automating analysis with scripted workflows using WDL and Cromwell
- Scaling up workflow execution in the cloud, including parallelization and cost optimization
- Interactive analysis in the cloud using Jupyter notebooks
- Secure collaboration and computational reproducibility using Terra
"Synopsis" may belong to another edition of this title.
About the Author
Dr. Brian O'Connor is the Director of the Computational Genomics Platform at the University of California Santa Cruz (UCSC) Genomics Institute. There, he focuses on the development and deployment of large-scale, cloud-based systems for analyzing genomic data. These include the NHGRI AnVIL and NHLBI Bio Data Catalyst platforms as well as the Dockstore site for workflow and tool sharing. Brian is active in standards efforts and is the cochair of the Global Alliance for Genomics and Health Cloud Work Stream where he works on API standards for cloud interoperability. Brian joined UCSC from the Ontario Institute for Cancer Research where his previous projects included leading the technical implementation of worldwide, cloud-based analysis systems for the PanCancer Analysis of Whole Genomes project, creating the Dockstore, and managing a successful rebuild of the International Cancer Genome Consortium's Data Portal.
"About the title" may belong to another edition of this title.
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