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<body class="book toc2 toc-left">
<div id="header">
<div id="toc" class="toc2">
<div id="toctitle"></div>
<ul class="sectlevel1">
<li><a href="#_overview">Overview</a></li>
<li><a href="#_costs_and_licenses">Costs and licenses</a></li>
<li><a href="#_architecture">Architecture</a></li>
<li><a href="#_deployment_options">Deployment options</a></li>
<li><a href="#_predeployment_steps">Predeployment steps</a>
<ul class="sectlevel2">
<li><a href="#_technical_requirements">Technical requirements</a></li>
<li><a href="#_marketplace_subscription">Marketplace subscription</a></li>
</ul>
</li>
<li><a href="#_deployment_steps">Deployment steps</a></li>
<li><a href="#_postdeployment_steps">Postdeployment steps</a>
<ul class="sectlevel2">
<li><a href="#_test_the_deployment">Test the deployment</a></li>
<li><a href="#option-1-use-the-aws-cli">Option 1: Use the AWS CLI</a></li>
<li><a href="#option-2-use-the-aws-batch-console">Option 2: Use the AWS Batch Console</a></li>
</ul>
</li>
<li><a href="#best-practices-using-dragen-on-aws">Best practices for using DRAGEN on AWS</a></li>
<li><a href="#_security">Security</a></li>
<li><a href="#_troubleshooting">Troubleshooting</a></li>
<li><a href="#_faq">FAQ</a></li>
<li><a href="#additional-resources">Additional Resources</a></li>
<li><a href="#_customer_responsibility">Customer responsibility</a></li>
<li><a href="#_feedback">Feedback</a></li>
<li><a href="#_notices">Notices</a></li>
</ul>
</div>
</div>
<div id="content">
<div id="preamble">
<div class="sectionbody">
<h2 id="_illumina_dragen_on_aws" class="discrete text-center">Illumina DRAGEN on AWS</h2>
<h2 id="_partner_solution_deployment_guide" class="discrete text-left text-center">Partner Solution Deployment Guide</h2>
<div class="imageblock text-center">
<div class="content">
<img src="https://aws-quickstart.s3.amazonaws.com/docs/deployment-guide/aws-quickstart-deployment-graphic.png" alt="QS" width="80" height="80">
</div>
</div>
<div class="paragraph text-center">
<p><strong>July 2023</strong><br>
<em>John Smith, Illumina</em><br>
<em>Will Quiles, Olivia Choudhury, Aaron Friedman, and Vinod Shukla, AWS</em><br></p>
</div>
<div class="imageblock text-left image-container">
<div class="content">
<img src="https://aws-quickstart.s3.amazonaws.com/cfn-ps-illumina-dragen/docs/boilerplate/.images/aws-quickstart-graphic.png" alt="">
</div>
</div>
<div class="admonitionblock tip">
<table>
<tr>
<td class="icon">
<i class="fa icon-tip" title="Tip"></i>
</td>
<td class="content">
Refer to the <a href="https://github.com/aws-ia/cfn-ps-illumina-dragen" target="_blank" rel="noopener">GitHub repository</a> to view source files, report bugs, submit feature ideas, and post feedback about this Partner Solution. To comment on the documentation, refer to <a href="#_feedback">Feedback</a>.
</td>
</tr>
</table>
</div>
<div class="paragraph text-left">
<p>This Partner Solution was created by Illumina in collaboration with Amazon Web Services (AWS). <a href="https://aws.amazon.com/solutions/partners/" target="_blank" rel="noopener">Partner Solutions</a> are automated reference deployments that help people deploy popular technologies on AWS according to AWS best practices. If you’re unfamiliar with AWS Partner Solutions, refer to the <a href="https://fwd.aws/rA69w?" target="_blank" rel="noopener">AWS Partner Solution General Information Guide</a>.</p>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_overview">Overview</h2>
<div class="sectionbody">
<div class="paragraph">
<p>This guide covers the information you need to deploy the Illumina DRAGEN Partner Solution in the AWS Cloud.</p>
</div>
<div class="paragraph">
<p>This Partner Solution guide provides step-by-step instructions for deploying Dynamic Read Analysis for GENomics (DRAGEN) on the AWS Cloud. The Partner Solution is for users who would like to conduct bioinformatic analysis on next-generation sequencing data using DRAGEN on AWS.</p>
</div>
<div class="paragraph">
<p>This Partner Solution was created to get you up and running with DRAGEN Complete Suite (CS) on AWS.
DRAGEN CS offerings enable ultra-rapid analysis of next-generation sequencing (NGS) data, and significantly reduce the time
required to analyze genomic data while also improving accuracy.</p>
</div>
<div class="paragraph">
<p>DRAGEN CS includes <a href="http://edicogenome.com/pipelines/" target="_blank" rel="noopener">many bioinformatics pipelines</a> that
harness the power of the DRAGEN platform and provide highly optimized algorithms for mapping, aligning, sorting,
duplicate marking, and haplotype variant calling. These pipelines include DRAGEN Germline V2, DRAGEN Somatic V2
(Tumor and Tumor/Normal), DRAGEN Virtual Long Read Detection (VLRD), DRAGEN RNA Gene Fusion, DRAGEN Joint Genotyping,
and GATK Best Practices. The DRAGEN Germline V2 and DRAGEN Somatic V2 pipelines have improved accuracy in calling single
nucleotide polymorphisms (SNPs) and small insertions and deletions (INDELs) compared with industry standards. For
performance results, see the <a href="https://precision.fda.gov/challenges/1/view/results" target="_blank" rel="noopener">PrecisionFDA Hidden Treasures – Warm Up</a>
challenge and the <a href="https://blog.dnanexus.com/2018-03-08-how-to-train-your-dragen-evaluating-and-improving-edico-genomes-rapid-wgs-tools/" target="_blank" rel="noopener">DRAGEN evaluation</a> on the <em>Inside DNAnexus</em> blog.</p>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_costs_and_licenses">Costs and licenses</h2>
<div class="sectionbody">
<div class="paragraph">
<p>There is no cost to use this Partner Solution, but you will be billed for any AWS services or resources that this Partner Solution deploys. For more information, refer to the <a href="https://fwd.aws/rA69w?" target="_blank" rel="noopener">AWS Partner Solution General Information Guide</a>.</p>
</div>
<div class="paragraph">
<p>This Quick Start requires a subscription to the Amazon Machine Image (AMI) for <a href="https://aws.amazon.com/marketplace/pp/B07CZ3F5HY" target="_blank" rel="noopener">DRAGEN Complete Suite</a>, which is available with per-hour pricing from AWS Marketplace.</p>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_architecture">Architecture</h2>
<div class="sectionbody">
<div class="paragraph">
<p>Deploying this Partner Solution with default parameters builds the following DRAGEN environment in the
AWS Cloud.</p>
</div>
<div id="architecture" class="imageblock">
<div class="content">
<img src="docs/deployment_guide/images/image1.png" alt="architecture" width="733" height="427">
</div>
<div class="title">Figure 1. Partner Solution architecture for DRAGEN on AWS</div>
</div>
<div class="paragraph">
<p>The Partner Solution sets up the following:</p>
</div>
<div class="ulist">
<ul>
<li>
<p>A highly available architecture that spans two Availability Zones.*</p>
</li>
<li>
<p>A virtual private cloud (VPC) configured with public and private subnets according to AWS best practices. This provides the network architecture for DRAGEN deployment.*</p>
</li>
<li>
<p>An internet gateway to provide access to the internet.*</p>
</li>
<li>
<p>In the public subnets, managed NAT gateways to allow outbound internet access for resources in the private subnets.*</p>
</li>
<li>
<p>An AWS CodePipeline pipeline that builds a Docker image and uploads it into an Amazon Elastic Container Registry (Amazon ECR) repository that interfaces with AWS Batch and runs in the DRAGEN AMI.</p>
</li>
<li>
<p>Two AWS Batch compute environments: one for Amazon Elastic Compute Cloud (Amazon EC2) Spot instances and the other for On-Demand instances. In the default setting, On-Demand instances have been prioritized over Spot instances. In order to reduce computation cost, you can prioritize Spot instances over On-Demand instances by updating the compute environment order under the Job Queue option of AWS Batch in the console.</p>
</li>
<li>
<p>An AWS Batch job queue that prioritizes submission to the compute environment for Spot Instances to optimize for cost.</p>
</li>
<li>
<p>An AWS Batch job definition to run DRAGEN.</p>