Genomics in the Cloud: Using Docker,GATK,and WDL in Terra
by: Brian D. O’Connor,Geraldine A. Van der Auwera
Pages: 506 pages
Edition 版本: 1
Language 语言: English
Publisher finelybook 出版社: O’Reilly Media
Released: 2020-06-09
ISBN-10: 1491975199
ISBN-13: 9781491975190
Book Description
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
Foreword
Preface
1.Introduction
2.Genomics in a Nutshell: A Primer for Newcomers to the
Field
3.Computing Technology Basics for Life Scientists
4.First Steps in the Cloud
5.First Steps with GATK
6.GATK Best Practices for Germline Short Variant Discovery
7.GATK Best Practices for Somatic Variant Discovery
8.Automating Analysis Execution with Workflows
9.Deciphering Real Genomics Workflows
10.Running Single Workflows at Scale with Pipelines APl
11.Running Many Workflows Conveniently in Terra
12.Interactive Analysis in Jupyter Notebook
13.Assembling Your Own Workspace in Terra
14.Making a Fully Reproducible Paper
Glossary
Index
