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图书信息
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云端基因组学
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ISBN: | 9787564195878 |
定价: | ¥148.00 |
作者: | Geraldine A. Van der Auwera,Brian D. O'Connor著 |
出版社: | 东南大学出版社 |
出版时间: | 2021年08月 |
版次: | 影印版 |
开本: | 24cm |
页数: | 24,467页 |
中图法: | Q343.2 |
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453
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2024-04-22
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图书简介 | 基因组学领域的数据正在剧增。在短短几年内,美国国家卫生研究院(National Institutes of Health,NIH)等组织托管的基因组数据已经超过了50PB(5000万GB),这些组织正在转向云基础架构,以便将数据提供给研究团体。你该如何调整分析工具和协议来访问和分析云端的海量数据?
通过这本实用书籍,研究人员将学会如何使用基因组分析工具包(Genome Analysis Toolkit,GATK)、Docker、WDL、Terra等开源工具来处理基因组学算法。GATK用户社区的长期监理人Geraldine Van der Auwera和加州大学圣克鲁兹基因组学研究所的Brian O’Connor会指导你完成这一过程。你将通过使用真实数据和相关领域的基因组学算法展开学习。 |
目录 | Foreword Preface 1. Introduction The Promises and Challenges of Big Data in Biology and Life Sciencer/> Infrastructure Challenger/> Toward a Cloud-Based Ecosystem for Data Sharing and Analysir/> Cloud-Hosted Data and Compute Platforms for Research in the Life Sciencer/> Standardization and Reuse of Infrastructure Being FAIR Wrap-Up and Next Stepr/>2. Genomics in a Nutshell: A Primer for Newcomers to the Field Introduction to Genomicr/> The Gene as a Discrete Unit of Inheritance (Sort Of) The Central Dogma of Biology: DNA to RNA to Protein The Origins and Consequences of DNA Mutationr/> Genomics as an Inventory of Variation in and Among Genomer/> The Challenge of Genomic Scale, by the Numberr/> Genomic Variation The Reference Genome as Common Framework Physical Classification of Variantr/> Germline Variants Versus Somatic Alterationr/> High-Throughput Sequencing Data Generation From Biological Sample to Huge Pile of Read Data Types of DNA Libraries: Choosing the Right Experimental Design Data Processing and Analysir/> Mapping Reads to the Reference Genome Variant Calling Data Quality and Sources of Error Functional Equivalence Pipeline Specification Wrap-Up and Next Stepr/>3. Computing Technology Basics for Life Scientistr/> Basic Infrastructure Components and Performance Bottleneckr/> Types of Processor Hardware: CPU, GPU, TPU, FPGA, OMG Levels of Compute Organization: Core, Node, Cluster, and Cloud ressing Performance Bottleneckr/> Parallel Computing Parallelizing a Simple Analysir/> From Cores to Clusters and Clouds: Many Levels of Parallelir/> Trade-Offs of Parallelism: Speed, Efficiency, and Cor/> Pipelining for ParaUelization and Automation Workflow Languager/> Popular Pipelining Languages for Genomicr/> Workflow Management Systemr/> Virtualization and the CIoud VMs and Containerr/> Introducing the Cloud Categories of Research Use Cases for Cloud Servicer/> Wrap-Up and Next Stepr/>4. First Steps in the Cloud Setting Up Your Google Cloud Account and First Project Creating a Project Che Your Billing Account and Activating Free Creditr/> Running Basic Commands in Google Cloud Shell Logging in to the Cloud Shell VM Using gsutil to Access and Manage Filer/> Pulling a Docker Image and Spinning Up the Container Mounting a Volume to Access the Filesystem from Within the Container Setting Up Your Own Custom VM Creating and Configuring Your VM Instance Logging into Your VM by Using SSH Che Your Authentication Copying the Book Materials to Your VM Installing Docker on Your VM Setting Up the GATK Container Image …… 6. GATK Best Practices for Germline Short Variant Discovery 7. GATK Best Practices for Somatic Variant Discovery 8. Automatina Analysis Execution with Workflowr/>9. Deciphering Real Genomics Workflowr/>10. Running Single Workflows at Scale with Pipelines API 11. Running Many Workflows Conveniently in Terra 12. Interactive Analysis in Jupyter Notebook 13. Asling Your Own Workspace in Terra 14. M a Fully Reproducible Paper Glossary Index
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