From the Preface If cloud technology is the future of biomedical science, then for genomics, the future is already here. Genomics is the first biomedical discipline to move en masse to the cloud. Perhaps inevitably so, given that it was the first to experience explosive growth in data generation, leading to rapidly escalating compute and storage requirement issues that a cloud infrastructure is ideally positioned to address. Major genomic datasets and their derived resources are now available in the cloud, and many tools like the industry-leading Genome Analysis Toolkit (GATK) produced by the Broad Institute are now offered in forms optimized to run efficiently on a cloud infrastructure. As a result, many researchers making use of genomic data and related analysis tools are now or will soon be confronted with the need to learn to use cloud resources, which can represent a huge challenge to many. Meanwhile, many informatics and bioinformatics support staff are being pulled in to help researchers to achieve this transition, sometimes with only minimal or no training relevant to the science of genomics. Taken together, these two populations form a continuum of people who need to get on the same page and work together to solve the challenges they face. Purpose, Scope, and Intended Audience of This Book With this book, we aim to provide a hands-on orientation tour of major tools, mechanisms, and processes involved in performing genomic analysis in the cloud that can serve as a middle ground for the majority of people on this spectrum. We try to assume as little prior knowledge as possible, and we provide two primer-style chapters, one focused on genomics and one on technology, to ensure that everyone has a firm grounding in the fundamental concepts we rely on from both domains. In addition, we deliberately chose a particular open source technology stack—GATK, Workflow Description Language (WDL), Terra, Docker, and Google Cloud Platform—that provides end-to-end functionality and is backed by robust user support systems in order to ensure a successful educational experience. To be clear, this book is not intended to be comprehensive, either in terms of tooling options or the scientific scope of genomic analyses. Our operational definition of genomics, centered on variant discovery and immediately related analyses, is intentionally narrow; and for every step of the processes we describe, there often exist several, if not many, alternative tools that you could substitute for those we chose to showcase. However, we designed the topics and exercises presented here to provide patterns and takeaways that are largely transferable and extensible to other tools and analyses in order to maximize their long-term value to readers. In addition, we plan to release a series of companion blog posts and other online materials that will show complementary approaches using different platforms and technologies; see the book’s GitHub repository and its companion website.
✔ Author(s): Geraldine Van der Auwera,Brian O'Connor
✔ Title: Genomics in the Cloud: Using Docker, GATK, and WDL in Terra
✔ Rating : 4.2 out of 5 base on (25 reviews)
✔ ISBN-10: 1491975199
✔ Language: English
✔ Format ebook: PDF, EPUB, Kindle, Audio, HTML and MOBI
✔ Device compatibles: Android, iOS, PC and Amazon Kindle
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