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Genomics in the cloud
Paperback
€92.99
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- Book Synopsis
- Data in the genomics field is booming. In just a few years, organizations such as the National Institutes of Health (NIH) will host 50+ petabytesâ??or over 50 million gigabytesâ??of genomic data, and theyâ??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 Oâ??Connor of the UC Santa Cruz Genomics Institute, guide you through the process. Youâ??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
- About The Author
- Dr. Geraldine A. Van der Auwera is the Director of Outreach and Communication for the Data Sciences Platform (DSP) at the Broad Institute of MIT and Harvard. As part of her outreach role, she serves as an educator and advocate for researchers who use DSP software and services including GATK, the Broad's industry-leading toolkit for variant discovery analysis; the Cromwell/WDL workflow management system; and Terra.bio, a cloud-based analysis platform that integrates computational resources, methods repository and data management in a user-friendly environment. Van der Auwera was originally trained as a microbiologist, earning her Ph.D. in Biological Engineering from the Université catholique de Louvain (UCL) in Belgium in 2007, then surviving a 4-year postdoctoral stint at Harvard Medical School. She joined the Broad Institute in 2012 to become Benevolent Dictator For Life of the GATK user community, leaving behind the bench and pipette work forever.
- Product Details
-
- ISBN
- 9781491975190
- Format
- Paperback
- Publisher
- O'Reilly, (23 April 2020)
- Number of Pages
- 493
- Weight
- 666 grams
- Language
- English
- Dimensions
- 233 x 178 x 15 mm
- Categories: