Genomics in the Cloud

The book provides practical guidance for researchers to work with genomics algorithms in the cloud, using open-source tools such as the Genome Analysis Toolkit (GATK), Docker, WDL, and Terra. It covers essential background information, cloud computing operations, GATK usage, automated analysis with scripted workflows, scaling up workflow execution, interactive analysis with Jupyter notebooks, secure collaboration, and computational reproducibility.

Format: Paperback / softback
Length: 475 pages
Publication date: 24 April 2020
Publisher: O'Reilly Media, Inc, USA

The genomics field is experiencing a remarkable surge in data, with organizations like the National Institutes of Health (NIH) poised to host over 50 million gigabytes of genomic data in the coming years. To meet the demand for efficient access and analysis of this vast amount of data, researchers are turning to cloud infrastructure. In this comprehensive book, experts guide researchers in adapting analysis tools and protocols to work seamlessly in the cloud.

The book begins by providing a foundational understanding of genomics and computing technology, covering essential concepts and tools. It then delves into basic cloud computing operations, enabling researchers to set up and manage cloud environments effectively. The authors introduce the Genome Analysis Toolkit (GATK), a widely used open-source tool for genomics analysis, and demonstrate its usage through three major GATK Best Practices pipelines. They also explore the automation of analysis with scripted workflows using Workflow Description Language (WDL) and Cromwell, enabling efficient and reproducible execution of genomics workflows.

Scaling up workflow execution in the cloud is a crucial aspect, and the book covers parallelization and cost optimization techniques to maximize computational resources. It also introduces interactive analysis in the cloud using Jupyter notebooks, providing a seamless platform for data exploration and analysis. Additionally, the book emphasizes secure collaboration and computational reproducibility using Terra, a distributed computing platform designed for genomics data management.

By following the step-by-step instructions and real-world examples provided in this book, researchers will gain the skills and knowledge necessary to work with genomics algorithms in the cloud. Whether they are beginners or experienced practitioners, this practical guide will empower them to leverage the power of cloud infrastructure for efficient and impactful genomics research.

Weight: 852g
Dimension: 177 x 234 x 29 (mm)
ISBN-13: 9781491975190