Genomics in the AWS Cloud: Performing Genome Analysis Using Amazon Web Services

Cover
Title Page
Copyright Page
Contents at a Glance
Contents
Introduction
	Who Should Read This Book
	Genomics
	Cloud Computing and AWS
	What You’ll Learn from This Book
		How This Book Is Organized
		How to Use This Book
	Our Story
	Getting Under Way
		How to Contact Wiley and the Authors
Chapter 1 Why Do Genome Analysis Yourself  When Commercial Offerings Exist?
	Commercial Sequencing Services
	Typical Results
	Summary
Chapter 2 A Crash Course in Molecular Biology
	DNA
	DNA at Work: RNA and Proteins
	Inheritance
	Summary
Chapter 3 Obtaining Your Genome
	Preparing to Have Your Genome Sequenced
		Can It Affect My Insurance?
		Privacy
		Humility and Levelheadedness
		Validation with a Clinically Accredited Test
		Alternatives to Using Your Own Genome
	Specifying Lab Work
		Depth
		Sample Type
		Type of Output Files
		Sequencing Technology
		Genome vs. Exome vs. SNP Arrays
	Engaging a Laboratory
	Getting a Tissue Sample for DNA Extraction
		Rules and Regulations
		Do-It-Yourself Phlebotomy
		Legal Considerations
	Shipping the Sample
	Receiving the Results
		Sequences and Quality Control Information
		Alignment Information
		Variation Information
	Summary
Chapter 4 The Bioinformatics Workflow
	Extraction of DNA
		Deriving Nucleated Cells from Whole Blood
		Processing Nucleated Cells
	FASTA Files
	FASTQ Files
		Phred Scores
		ASCII Encoding of Phred Scores
	Alignment to a Reference Genome
	Reference Genomes
	Quality Control
	Trimming
	The Alignment Process
	Marking Duplicates
	Recalibrating Base Quality Score
	Calling SNVs and Indel Variants
	Annotating SNVs and Indel Variants
	Prioritizing Variants
	Inheritance Analysis
	Identifying SVs and CNVs
	Bioinformatics Workflow
	Summary
Chapter 5 AWS Services for Genome Analysis
	General Concepts
		Networking
			AWS Functionalities
			AWS Accounts
			Virtual Private Cloud
			Subnets
			Elastic IP Addresses
	Custom Environments
		Storage
			S3
			Glacier
		Computing
			Elastic Compute Cloud
			Containers
			Lambda Functions
		Workflow Management
			AWS Batch
			AWS Step Functions
			Simple Workflow Service
			Third-Party Solutions
	Summary
Chapter 6 Building Your Environment in the AWS Cloud
	Setting Up a Virtual Private Cloud
	Setting Up and Launching an EC2 Instance
		Shutting Down an Instance to Save Money
	Setting Up S3 Buckets
	Configuring Your Account Securely
		Turning On Multifactor Authentication
		Establishing an AWS IAM Password Policy
	Creating Groups
	Creating Users
	Setting Up Your Client Environment
		Connecting to an EC2 Instance
			Connecting from macOS or Unix/Linux
			Connecting from Windows
		Making S3 Buckets Available Locally
			Mounting an S3 Bucket as a Windows Drive
			Mounting an S3 Bucket Under macOS and Linux
	Summary
Chapter 7 Linux and AWS Command-Line Basics for Genomics
	Selecting a Linux Distribution
	Accessing Your AWS Linux Instance from Your Local Computer
		From Windows
		From macOS
		Options for Setting Up Linux on Your Personal Computer
	Getting Familiar with the Command Line
		Absolute and Relative References
		Manipulating Files
	Transferring Files to and from Your AWS Instance
		Keyboard Shortcuts
	Running Programs in the Background
	Understanding File Permissions
	Compressing and Archiving Files
		Compression
		Grep
		Pipes and Redirection Operators
		Text Processing Utilities: awk and sed
	Managing Linux
		Package Management Systems
	The AWS Command-Line Interface
		Installing the AWS CLI Environment
			Windows
			macOS and Linux
		Configuring the AWS CLI
			Setting the Configuration at the Command Line
			Storing the Configuration in the Configuration File
		Testing Your Installation
	AWS CLI Essentials
	An Alternative Approach: AWS Systems Manager
	Summary
Chapter 8 Processing theSequencing Data
	Getting from Data to Information
		Aligning to the Reference Genome
		Making Adjustments and Refinements to the Aligned Reads in the BAM File
		Identifying the Small Differences and Recording Them in the VCF File
		Making Adjustments and Refinements to the Variants in the VCF File
		Annotating the SNVs and Indels
		Prioritizing the Variants to Identify the Most Consequential Ones
		Trio Analysis and Inheritance Analysis
		Identifying and Annotating SVs and CNVs
	Setting Up AWS Services and Data Storage
		Copying the FASTQ Files
		Installing Docker and Containers
	Summary
Chapter 9 Visualizing the Genome
	Introducing Genome Visualizers
	Installing the IGV Desktop Visualizer
		Connecting the IGV Visualizer to Our AWS Data
		Loading Data into the IGV Visualizer
		Visualizing Aligned Sequencing Reads in IGV
		Have a CIGAR
	Analyzing Variants in IGV
	Summary
Chapter 10 Containerizing Your Workflow on the Desktop
	Introducing Containerization
	Understanding and Using Docker
		Installing Docker on Your Local Machine
		Downloading a Docker Image
		Viewing Available Docker Images
		Running a Docker Container Interactively
		Removing a Docker Image
		More on Using the Docker Hub
			Containers for Genomics Work
	Summary
Chapter 11 Variants and Applications
	Polygenic Risk Scores
		Genome-wide Association Studies
		Calculating a Polygenic Score
	Metagenomics
	AlphaFold
		Predicting Protein Structure from Protein Sequence—A 50-Year Puzzle
		Installing and Running AlphaFold
		Viewing and Comparing AlphaFold Results
	Summary
Chapter 12 Cancer Genomics
	Somatic Genomes
	Cancer
		Oncogenes
		Tumor Suppressors
	The Promise and Reality of Cancer Precision Medicine
		Somatic or Germline? Cancer Predisposition
		Chromothripsis
		Epigenetics of Cancer
		Mechanisms of Cancer
	Samples
	Somatic Variant Analysis
	Copy Number Changes
	Measuring Tumor Genomic Instability
	Summary
	Notes
Index
EULA