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Genomics in the Cloud

2020-04-02 Computers
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Release : 2020-04-02
Genre : Computers
Kind : eBook
Book Rating : 164/5 ( reviews)

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Book Synopsis Genomics in the Cloud by : Geraldine A. Van der Auwera

Download or read book Genomics in the Cloud written by Geraldine A. Van der Auwera. This book was released on 2020-04-02. Available in PDF, EPUB and Kindle. Book excerpt: 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

Genomics in the Cloud

2020-04-02 Science
Download Genomics in the Cloud PDF Online Free

Author :
Release : 2020-04-02
Genre : Science
Kind : eBook
Book Rating : 148/5 ( reviews)

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Book Synopsis Genomics in the Cloud by : Geraldine A. Van der Auwera

Download or read book Genomics in the Cloud written by Geraldine A. Van der Auwera. This book was released on 2020-04-02. Available in PDF, EPUB and Kindle. Book excerpt: Data in the genomics field is booming. In just a few years, organizations such as the National Institutes of Health (NIH) will host 50+ petabytesâ??or over 50 million gigabytesâ??of genomic data, and theyâ??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 Oâ??Connor of the UC Santa Cruz Genomics Institute, guide you through the process. Youâ??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

Genomics in the Cloud

2020
Download Genomics in the Cloud PDF Online Free

Author :
Release : 2020
Genre :
Kind : eBook
Book Rating : 183/5 ( reviews)

GET EBOOK


Book Synopsis Genomics in the Cloud by : Geraldine Van der Auwera

Download or read book Genomics in the Cloud written by Geraldine Van der Auwera. This book was released on 2020. Available in PDF, EPUB and Kindle. Book excerpt: 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 52.4 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 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. Brian O'Connor of the UC Santa Cruz Genomics Institute and Geraldine Van der Auwera, longtime custodian of the GATK user community, guide you through the process. You'll learn by working with real data and genomics algorithms from the field. This book takes you through: Essential genomics and computing technology background Basic cloud computing operations Getting started with GATK Three major GATK best practices for variant discovery 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.

Genomics Analysis with Spark, Docker and Clouds

2020-02-04 Computers
Download Genomics Analysis with Spark, Docker and Clouds PDF Online Free

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Release : 2020-02-04
Genre : Computers
Kind : eBook
Book Rating : 190/5 ( reviews)

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Book Synopsis Genomics Analysis with Spark, Docker and Clouds by : Brian D. O'Connor

Download or read book Genomics Analysis with Spark, Docker and Clouds written by Brian D. O'Connor. This book was released on 2020-02-04. Available in PDF, EPUB and Kindle. Book excerpt: Genomics researchers today are faced with an ever-increasing amount of data to analyze, and yet they have a difficult time leveraging modern frameworks and technologies (like Spark and cloud infrastructure) to efficiently and accurately analyze their data. This practical guide provides the guidance these researchers need. With this book, you'll learn how to combine algorithms designed for genomics with the leading tool for big data--Spark--and the ascendant paradigm of working in the cloud with Docker.

Genomics in the AWS Cloud

2023-05-02 Computers
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Release : 2023-05-02
Genre : Computers
Kind : eBook
Book Rating : 371/5 ( reviews)

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Book Synopsis Genomics in the AWS Cloud by : Catherine Vacher

Download or read book Genomics in the AWS Cloud written by Catherine Vacher. This book was released on 2023-05-02. Available in PDF, EPUB and Kindle. Book excerpt: Perform genome analysis and sequencing of data with Amazon Web Services Genomics in the AWS Cloud: Analyzing Genetic Code Using Amazon Web Services enables a person who has moderate familiarity with AWS Cloud to perform full genome analysis and research. Using the information in this book, you’ll be able to take a FASTQ file containing raw data from a lab or a BAM file from a service provider and perform genome analysis on it. You’ll also be able to identify potentially pathogenic gene sequences. • Get an introduction to Whole Genome Sequencing (WGS) • Make sense of WGS on AWS • Master AWS services for genome analysis Some key advantages of using AWS for genomic analysis is to help researchers utilize a wide choice of compute services that can process diverse datasets in analysis pipelines. Genomic sequencers that generate raw data files are located in labs on premises and AWS provides solutions to make it easy for customers to transfer these files to AWS reliably and securely. Storing Genomics and Medical (e.g., imaging) data at different stages requires enormous storage in a cost-effective manner. Amazon Simple Storage Service (Amazon S3), Amazon Glacier, and Amazon Elastics Block Store (Amazon EBS) provide the necessary solutions to securely store, manage, and scale genomic file storage. Moreover, the storage services can interface with various compute services from AWS to process these files. Whether you’re just getting started or have already been analyzing genomics data using the AWS Cloud, this book provides you with the information you need in order to use AWS services and features in the ways that will make the most sense for your genomic research.

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