Illumina DRAGEN Bio-It Platform on the AWS Cloud

Quick Start Reference Deployment

QS

April 2021
Illumina
Will Quiles, Olivia Choudhury, Aaron Friedman, and Vinod Shukla, AWS Quick Start team

Visit our GitHub repository for source files and to post feedback, report bugs, or submit feature ideas for this Quick Start.

This Quick Start was created by Illumina in collaboration with Amazon Web Services (AWS). Quick Starts are automated reference deployments that use AWS CloudFormation templates to deploy key technologies on AWS, following AWS best practices.

Overview

This Quick Start guide provides step-by-step instructions for deploying Dynamic Read Analysis for GENomics (DRAGEN) on the AWS Cloud.

The Quick Start is for users who would like to conduct bioinformatic analysis on next-generation sequencing data using DRAGEN on AWS.

Amazon may share user-deployment information with the AWS Partner that collaborated with AWS on the Quick Start.

Illumina DRAGEN Bio-It Platform on AWS

This Quick Start was created to get you up and running with DRAGEN Bio-It Platform on AWS. DRAGEN 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.

It includes bioinformatics pipelines that provide highly optimized algorithms for mapping, aligning, sorting, duplicate marking, and haplotype variant calling. These pipelines include Germline, Somatic (tumor and tumor/normal), RNA, Single Cell RNA, Methylation, Joint Genotyping, and DRAGEN-GATK. The DRAGEN mapping and variant calling 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 PrecisionFDA Truth Challenge V2, where DRAGEN won best performance in all regions and difficult-to-map regions categories.

AWS costs

You are responsible for the cost of the AWS services and any third-party licenses used while running this Quick Start. There is no additional cost for using the Quick Start.

The AWS CloudFormation templates for Quick Starts include configuration parameters that you can customize. Some of the settings, such as the instance type, affect the cost of deployment. For cost estimates, see the pricing pages for each AWS service you use. Prices are subject to change.

After you deploy the Quick Start, create AWS Cost and Usage Reports to deliver billing metrics to an Amazon Simple Storage Service (Amazon S3) bucket in your account. These reports provide cost estimates based on usage throughout each month and aggregate the data at the end of the month. For more information, see What are AWS Cost and Usage Reports?

Software licenses

This Quick Start requires a subscription to the Amazon Machine Image (AMI) for DRAGEN Bio-IT platform, which is available with per-hour pricing from AWS Marketplace.

Architecture

Deploying this Quick Start for a new virtual private cloud (VPC) with default parameters builds the following DRAGEN environment in the AWS Cloud.

architecture
Figure 1. Quick Start architecture for DRAGEN on AWS

The Quick Start sets up the following:

  • A highly available architecture that spans two Availability Zones.*

  • A virtual private cloud (VPC) configured with public and private subnets according to AWS best practices. This provides the network architecture for DRAGEN deployment.*

  • An internet gateway to provide access to the internet.*

  • In the public subnets, managed NAT gateways to allow outbound internet access for resources in the private subnets.*

  • 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.

  • 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.

  • An AWS Batch job queue that prioritizes submission to the compute environment for Spot Instances to optimize for cost.

  • An AWS Batch job definition to run DRAGEN.

  • AWS Identity and Access Management (IAM) roles and policies for the AWS Batch jobs to run.

* The template that deploys the Quick Start into an existing VPC skips the tasks marked by asterisks and prompts you for your existing VPC configuration.

Planning the deployment

Specialized knowledge

This deployment requires a moderate level of familiarity with AWS services. If you’re new to AWS, see Getting Started Resource Center and AWS Training and Certification. These sites provide materials for learning how to design, deploy, and operate your infrastructure and applications on the AWS Cloud.

Before you deploy this Quick Start, we recommend that you become familiar with the following AWS services.

AWS account

If you don’t already have an AWS account, create one at https://aws.amazon.com by following the on-screen instructions. Part of the sign-up process involves receiving a phone call and entering a PIN using the phone keypad.

Your AWS account is automatically signed up for all AWS services. You are charged only for the services you use.

Resource quotas

If necessary, request service quota increases for the following resources. You might need to request increases if your existing deployment currently uses these resources and if this Quick Start deployment could result in exceeding the default quotas. The Service Quotas console displays your usage and quotas for some aspects of some services. For more information, see What is Service Quotas? and AWS service quotas.

Resource This deployment uses

VPCs

1

Elastic IP addresses

2

Security groups

1

AWS Identity and Access Management (IAM) roles

8

f1.4xlarge instances

1

Supported Regions

This Quick Start supports the following Regions:

  • us-east-1, US East (N. Virginia)

  • us-west-1, US West (N. California)

  • us-west-2, US West (Oregon)

  • ap-southeast-2, Asia Pacific (Sydney)

This Quick Start uses Amazon EC2 F1 instances, which aren’t available in all AWS Regions. For a list of supported regions, see AWS Regional Table webpage.
Certain Regions are available on an opt-in basis. For more information, see Managing AWS Regions.

EC2 key pairs

Make sure that at least one Amazon EC2 key pair exists in your AWS account in the Region where you plan to deploy the Quick Start. Make note of the key pair name. You need it during deployment. To create a key pair, see Amazon EC2 key pairs and Linux instances.

For testing or proof-of-concept purposes, we recommend creating a new key pair instead of using one that’s already being used by a production instance.

IAM permissions

Before launching the Quick Start, you must sign in to the AWS Management Console with IAM permissions for the resources that the templates deploy. The AdministratorAccess managed policy within IAM provides sufficient permissions, although your organization may choose to use a custom policy with more restrictions. For more information, see AWS managed policies for job functions.

Prerequisites

Technical requirements

  • Limit increases for F1 instances. DRAGEN runs on Amazon EC2 F1 instances because it requires a field-programmable gate array (FPGA). This Quick Start supports f1.2xlarge, f1.4xlarge, and f1.16xlarge instance types. You should request limit increases for F1 instances, to support the maximum number of simultaneous DRAGEN jobs that you expect to run.

  • S3 bucket for genomic data. You must have an Amazon Simple Storage Service (Amazon S3) bucket in the AWS Region where you plan to deploy the Quick Start. This S3 bucket should contain:

    • The genomic input datasets that you want to run in the Quick Start environment

    • The DRAGEN-specific reference hash table directories that are provided by Illumina or that you create from FASTA files. For instructions on how to create reference hash table directories, refer to DRAGEN Bio-IT Platform User Guide

    • An output folder for DRAGEN job outputs such as the binary alignment map (BAM) and variant call format (VCF) files

    You’ll be prompted for the bucket name when you deploy the Quick Start. The appropriate roles and policies to read from, and write to, this S3 genomics bucket are created during the Quick Start deployment.

Deployment options

This Quick Start provides two deployment options:

  • Deploy DRAGEN into a new VPC. This option builds a new AWS environment consisting of the VPC, subnets, NAT gateways, security groups, bastion hosts, and other infrastructure components. It then deploys DRAGEN into this new VPC.

  • Deploy DRAGEN into an existing VPC. This option provisions DRAGEN in your existing AWS infrastructure.

The Quick Start provides separate templates for these options. It also lets you configure Classless Inter-Domain Routing (CIDR) blocks, instance types, and DRAGEN settings, as discussed later in this guide.

Deployment steps

Sign in to your AWS account

  1. Sign in to your AWS account at https://aws.amazon.com with an IAM user role that has the necessary permissions. For details, see Planning the deployment earlier in this guide.

  2. Make sure that your AWS account is configured correctly, as discussed in the Technical requirements section.

Subscribe to the DRAGEN AMI

This Quick Start requires a subscription to the AMI for DRAGEN in AWS Marketplace.

  1. Sign in to your AWS account.

  2. Open the page for the DRAGEN AMI in AWS Marketplace, and then choose Continue to Subscribe.

  3. Review the terms and conditions for software usage, and then choose Accept Terms.
    A confirmation page loads, and an email confirmation is sent to the account owner. For detailed subscription instructions, see the AWS Marketplace documentation.

  4. When the subscription process is complete, exit out of AWS Marketplace without further action. Do not provision the software from AWS Marketplace—the Quick Start deploys the AMI for you.

Launch the Quick Start

If you’re deploying DRAGEN into an existing VPC, make sure that your VPC has two private subnets in different Availability Zones for the workload instances and that the subnets aren’t shared. This Quick Start doesn’t support shared subnets. These subnets require NAT gateways in their route tables to allow the instances to download packages and software without exposing them to the internet. Also make sure that the domain name option in the DHCP options is configured as explained in DHCP options sets. You provide your VPC settings when you launch the Quick Start.

Each deployment takes about 15 minutes to complete.

  1. Sign in to your AWS account, and choose one of the following options to launch the AWS CloudFormation template. For help with choosing an option, see Deployment options earlier in this guide.

Deploy DRAGEN into a new VPC on AWS

View template

Deploy DRAGEN into an existing VPC on AWS

View template

  1. Check the AWS Region that’s displayed in the upper-right corner of the navigation bar, and change it if necessary. This Region is where the network infrastructure for DRAGEN is built. The template is launched in the us-east-1 Region by default. For other choices, see Supported Regions earlier in this guide.

  1. On the Create stack page, keep the default setting for the template URL, and then choose Next.

  2. On the Specify stack details page, change the stack name if needed. Review the parameters for the template. Provide values for the parameters that require input. For all other parameters, review the default settings and customize them as necessary. For details on each parameter, see the Parameter reference section of this guide. When you finish reviewing and customizing the parameters, choose Next.

  3. On the Configure stack options page, you can specify tags (key-value pairs) for resources in your stack and set advanced options. When you’re finished, choose Next.

  4. On the Review page, review and confirm the template settings. Under Capabilities, select the two check boxes to acknowledge that the template creates IAM resources and might require the ability to automatically expand macros.

  5. Choose Create stack to deploy the stack.

  6. Monitor the status of the stack. When the status is CREATE_COMPLETE, the DRAGEN deployment is ready.

  7. To view the created resources, see the values displayed in the Outputs tab for the stack.

Test the deployment

When the deployment is complete, you can verify the environment by running a DRAGEN job. This job reads the input datasets and the reference hash table from the S3 genomics data bucket you specified when you deployed the Quick Start, and outputs the analysis results into the designated output location in the S3 bucket. Note that the input datasets and reference hash table must be located in the same S3 bucket, the one specified during deployment.

As a quick test, we recommend using an input dataset consisting of a smaller FASTQ pair, such as one of the following data samples:

Use AWS Batch to launch the job either through the AWS Command Line Interface (AWS CLI) or the console. Provide the DRAGEN job parameters as commands (in the command array within the containerOverrides field in the AWS CLI or the Command field in the console). For a full list of options, see the Illumina DRAGEN Bio-It Platform Getting Started Guide or Illumina DRAGEN Bio-It Platform Bio-IT Platform User Guide available on the Illumina DRAGEN Bio-It Platform Bio-IT Platform Support Resources website.

Most of the options function exactly as they are described in the guide. However, for options that refer to local files or directories, provide the full path to the S3 bucket that contains the genomics data.

In the following sections, we’ve provided instructions for running an end-to-end DRAGEN job using both methods (AWS CLI and console). In this example, the DRAGEN job handles mapping, aligning, sorting, deduplication, and variant calling. An input dataset with a paired FASTQ file is used to generate a variant call format (VCF) output file.

Option 1: Use the AWS CLI

The simplest way to run a DRAGEN job by using the AWS CLI is to create an input JSON file that describes the job. Here’s an example of a JSON input file named e2e-job.json:

{
    "jobName": "e2e-job",
    "jobQueue": "dragen-queue",
    "jobDefinition": "dragen",
    "containerOverrides": {
        "vcpus": 16,
        "memory": 120000,
        "command": [
            "-f", "-r", "s3://<bucket/path-to-ref-ht>",
            "-1", "s3://<bucket/path-to-file/file1_1.fastq.gz>",
            "-2", "s3://<bucket/path-to-file/file1_2.fastq.gz>",
            "--RGID", "1",
            "--RGSM", <RGSM>,
            "--enable-bam-indexing", "true",
            "--enable-map-align-output", "true",
            "--enable-sort", "true",
            "--output-file-prefix", <PREFIX>,
            "--enable-map-align", "true",
            "--output-format", "BAM",
            "--output-directory", "s3://<bucket/path-to-output/>",
            "--enable-variant-caller", "true"
        ]
    },
    "retryStrategy": {
        "attempts": 1
    }
}

You can then launch the job from the command line by using the submit-job command and specifying the e2e-job.json file as input:

aws batch submit-job --cli-input-json file://e2e-job.json

You can submit multiple Batch jobs from the CLI. Here is an example with two JSON input files named e2e-job1.json and e2e-job2.json.

{
    "jobName": "e2e-job1",
    "jobQueue": "dragen-queue",
    "jobDefinition": "dragen",
    "containerOverrides": {
        "vcpus": 16,
        "memory": 120000,
        "command": [
            "-f", "-r", "s3://<bucket/path-to-ref-ht>",
            "-1", "s3://<bucket/path-to-file/file1_1.fastq.gz>",
            "-2", "s3://<bucket/path-to-file/file1_2.fastq.gz>",
            "--RGID", "1",
            "--RGSM", <RGSM>,
            "--enable-bam-indexing", "true",
            "--enable-map-align-output", "true",
            "--enable-sort", "true",
            "--output-file-prefix", <PREFIX>,
            "--enable-map-align", "true",
            "--output-format", "BAM",
            "--output-directory", "s3://<bucket/path-to-output/>",
            "--enable-variant-caller", "true"
        ]
    },
    "retryStrategy": {
        "attempts": 1
    }
}
{
    "jobName": "e2e-job2",
    "jobQueue": "dragen-queue",
    "jobDefinition": "dragen",
    "containerOverrides": {
        "vcpus": 16,
        "memory": 120000,
        "command": [
            "-f", "-r", "s3://<bucket/path-to-ref-ht>",
            "-1", "s3://<bucket/path-to-file/file1_1.fastq.gz>",
            "-2", "s3://<bucket/path-to-file/file1_2.fastq.gz>",
            "--RGID", "1",
            "--RGSM", <RGSM>,
            "--enable-bam-indexing", "true",
            "--enable-map-align-output", "true",
            "--enable-sort", "true",
            "--output-file-prefix", <PREFIX>,
            "--enable-map-align", "true",
            "--output-format", "BAM",
            "--output-directory", "s3://<bucket/path-to-output/>",
            "--enable-variant-caller", "true"
        ]
    },
    "retryStrategy": {
        "attempts": 1
    }
}

The following bash script can be used to submit the above two jobs.

#!/bin/bash
echo "Starting first job ..."
aws batch submit-job --cli-input-json e2e-job1.json > ./job-output-log
echo "Starting second job ..."
aws batch submit-job --cli-input-json e2e-job1.json >> ./job-output-log
echo "No more jobs pending!"

Option 2: Use the AWS Batch Console

To run the DRAGEN job from the console:.

  1. Open the AWS Batch console at https://console.aws.amazon.com/batch/

  2. From the navigation bar, choose the AWS Region you used for the Quick Start deployment.

  3. In the navigation pane, choose Jobs, Submit new job.

  4. Fill out these fields, as shown in Figure 2:

    • Job name: Enter a unique name for the job.

    • Job definition: Choose the DRAGEN job definition that was created by the Quick Start and displayed in the Outputs tab of the AWS CloudFormation console in step 3(9).

    • Job queue: Choose dragen-queue, which was created by the Quick Start.

    • Job type: Choose Single.

    • Command: Specify the DRAGEN-specific parameters shown in the JSON command array in option 1.

    • vCPUs, Memory, Job attempts, Execution timeout: Keep the defaults that are specified in the job definition.

    For more information, see the AWS Batch documentation.

  5. Choose Submit.

    runjob
    Figure 2. Running a DRAGEN job from the AWS Batch console
  6. Monitor the job status in the AWS Batch window to see if it succeeded or failed. For more information about job states and exit codes, see the AWS Batch documentation.

Best practices for using DRAGEN on AWS

For simplicity, we recommend that you create your S3 bucket in the AWS Region that you are deploying the Quick Start into. In some use cases, as outlined in the DRAGEN User Guide on the Illumina website you might need to attach EBS volumes to instances.  The DRAGEN guides are available as links from the DRAGEN Bio-IT Platform webpage in AWS Marketplace (see the Usage Information section on that page).

Security

DRAGEN doesn’t enforce any specific security requirements. However, for security, this Quick Start deploys DRAGEN into private subnets that aren’t externally reachable from outside the VPC (they can access the internet only through NAT gateways). Please consult your IT and security teams for image hardening, encryption, and other security requirements.

FAQ

Q. I encountered a CREATE_FAILED error when I launched the Quick Start.

A. If AWS CloudFormation fails to create the stack, we recommend that you relaunch the template with Rollback on failure set to No. (This setting is under Advanced in the AWS CloudFormation console, Options page.) With this setting, the stack’s state will be retained and the instance will be left running, so you can troubleshoot the issue.

Important When you set Rollback on failure to No, you will continue to incur AWS charges for this stack. Please make sure to delete the stack when you finish troubleshooting.

For additional information, see Troubleshooting AWS CloudFormation on the AWS website.

Q. I encountered a size limitation error when I deployed the AWS CloudFormation templates.

A. We recommend that you launch the Quick Start templates from the links in this guide or from another S3 bucket. If you deploy the templates from a local copy on your computer or from a non-S3 location, you might encounter template size limitations when you create the stack. For more information about AWS CloudFormation limits, see the AWS documentation.

Q. How can I find out whether my DRAGEN job has completed?

A. When you submit a DRAGEN job by using the AWS CLI or the AWS Batch console, as described previously in Test the deployment section, you will get an AWS Batch job ID. You should monitor the job status to check for completion. When the job has completed successfully, its job state will be displayed as SUCCEEDED and the outputs will be uploaded into the output S3 bucket location that is specified in the job. For more information about job states, see the AWS Batch documentation.

Q. What should I do if the DRAGEN job fails?

A. If your DRAGEN job fails, more information will be available in Amazon CloudWatch Logs. You can access the log either from the CloudWatch console (see Figure 3) or through the Log stream name link in the AWS Batch job (see Figure 4).

logCW
Figure 3. Accessing logs from the CloudWatch console
logBatch
Figure 4. Accessing logs from the AWS Batch console

When you run a DRAGEN job, you use the --output-directory parameter to specify an S3 output bucket, as described in Test the deployment section. If the DRAGEN job fails, more information about the failure is provided in the DRAGEN process output log, which is uploaded to the S3 bucket you specified. Look for the object in the S3 bucket that has the key name dragen_log_<timestamp>.txt for the output log.

Generally, DRAGEN process logs will give adequate information about failures, but if you need further help, please contact Illumina at techsupport@illumina.com.

Additional Resources

Customer responsibility

After you successfully deploy this Quick Start, confirm that your resources and services are updated and configured — including any required patches — to meet your security and other needs. For more information, see the AWS Shared Responsibility Model.

Parameter reference

Unless you are customizing the Quick Start templates for your own deployment projects, keep the default settings for the parameters labeled Quick Start S3 bucket name, Quick Start S3 bucket Region, and Quick Start S3 key prefix. Changing these parameter settings automatically updates code references to point to a new Quick Start location. For more information, see the AWS Quick Start Contributor’s Guide.

Parameters for deploying into an existing VPC

Table 1. Network Configuration
Parameter label (name) Default value Description

VPC ID (VPCID)

Requires input

The ID of your existing VPC (e.g., vpc-0343606e).

Private Subnet 1 ID (PrivateSubnet1ID)

Requires input

The ID of the private subnet in Availability Zone 1 in your existing VPC (e.g., subnet-a0246dcd).

Private Subnet 2 ID (PrivateSubnet2ID)

Requires input

The ID of the private subnet in Availability Zone 2 in your existing VPC (e.g., subnet-b58c3d67).

Table 2. DRAGEN Quick Start Configuration
Parameter label (name) Default value Description

Key Pair Name (KeyPairName)

Requires input

The name of an existing public/private key pair, which allows you to securely connect to your instance after it launches

Instance Type (InstanceType)

f1.4xlarge

Amazon EC2 instance type. DRAGEN requires an FPGA to run, so the instance type must be in the F1 instance family.

Spot Bid Percentage (BidPercentage)

50

The bid percentage set for your AWS Batch Managed Compute Environment with Spot Instances.

Min vCPUs (MinvCpus)

0

Minimum vCPUs for your AWS Batch Compute Environment. Recommend 0.

Max vCPUs (MaxvCpus)

Requires input

Maximum vCPUs for your AWS Batch Compute Environment

Desired vCPUs (DesiredvCpus)

0

Desired vCPUs for your AWS Batch Compute Environment. Recommend the same number as MinvCpus for cost-optimization.

Genomics Data Bucket (GenomicsS3Bucket)

Requires input

S3 bucket name for the bucket to which you’ll read and write genomics data.

AWS Batch Retry Number (RetryNumber)

1

Retry number for an AWS Batch job

Table 3. AWS Quick Start Configuration
Parameter label (name) Default value Description

Quick Start S3 Bucket Name (QSS3BucketName)

aws-quickstart

S3 bucket name for the Quick Start assets. Quick Start bucket name can include numbers, lowercase letters, uppercase letters, and hyphens (-). It cannot start or end with a hyphen (-).

Quick Start S3 bucket region (QSS3BucketRegion)

us-east-1

The AWS Region where the Quick Start S3 bucket (QSS3BucketName) is hosted. When using your own bucket, you must specify this value.

Quick Start S3 Key Prefix (QSS3KeyPrefix)

quickstart-illumina-dragen/

S3 key prefix for the Quick Start assets. Quick Start key prefix can include numbers, lowercase letters, uppercase letters, hyphens (-), and forward slash (/).

Parameters for deploying into a new VPC

Table 4. Network Configuration
Parameter label (name) Default value Description

Availability Zones (AvailabilityZones)

Requires input

The list of Availability Zones to use for the subnets in the VPC. The Quick Start uses two Availability Zones from your list and preserves the logical order you specify.

VPC CIDR (VPCCIDR)

10.0.0.0/16

The CIDR block for the VPC.

Private Subnet 1 CIDR (PrivateSubnet1CIDR)

10.0.0.0/19

The CIDR block for the private subnet located in Availability Zone 1.

Private Subnet 2 CIDR (PrivateSubnet2CIDR)

10.0.32.0/19

The CIDR block for the private subnet located in Availability Zone 2.

Public Subnet 1 CIDR (PublicSubnet1CIDR)

10.0.128.0/20

The CIDR block for the public (DMZ) subnet 1 located in Availability Zone 1.

Public Subnet 2 CIDR (PublicSubnet2CIDR)

10.0.144.0/20

The CIDR block for the public (DMZ) subnet 2 located in Availability Zone 2.

Table 5. DRAGEN Quick Start Configuration
Parameter label (name) Default value Description

Key Pair Name (KeyPairName)

Requires input

The name of an existing public/private key pair, which allows you to securely connect to your instance after it launches.

Instance Type (InstanceType)

f1.4xlarge

Amazon EC2 instance type for DRAGEN in the AWS Batch Compute Environment.

Spot Bid Percentage (BidPercentage)

50

The bid percentage set for your AWS Batch Managed Compute Environment with Spot Instances.

Min vCPUs (MinvCpus)

0

Minimum vCPUs for your AWS Batch Compute Environment. Recommend 0.

Max vCPUs (MaxvCpus)

Requires input

Maximum vCPUs for your AWS Batch Compute Environment.

Desired vCPUs (DesiredvCpus)

0

Desired vCPUs for your AWS Batch Compute Environment. Recommend the same number as MinvCpus for cost-optimization.

Genomics Data Bucket (GenomicsS3Bucket)

Requires input

S3 bucket name for the bucket to which you’ll read and write genomics data.

AWS Batch Retry Number (RetryNumber)

1

Retry number for an AWS Batch job.

Table 6. AWS Quick Start Configuration
Parameter label (name) Default value Description

Quick Start S3 Bucket Name (QSS3BucketName)

aws-quickstart

S3 bucket name for the Quick Start assets. Quick Start bucket name can include numbers, lowercase letters, uppercase letters, and hyphens (-). It cannot start or end with a hyphen (-).

Quick Start S3 bucket region (QSS3BucketRegion)

us-east-1

The AWS Region where the Quick Start S3 bucket (QSS3BucketName) is hosted. When using your own bucket, you must specify this value.

Quick Start S3 Key Prefix (QSS3KeyPrefix)

quickstart-illumina-dragen/

S3 key prefix for the Quick Start assets. Quick Start key prefix can include numbers, lowercase letters, uppercase letters, hyphens (-), and forward slash (/).

Send us feedback

To post feedback, submit feature ideas, or report bugs, use the Issues section of the GitHub repository for this Quick Start. To submit code, see the Quick Start Contributor’s Guide.

Quick Start reference deployments

GitHub repository

Visit our GitHub repository to download the templates and scripts for this Quick Start, to post your comments, and to share your customizations with others.


Notices

This document is provided for informational purposes only. It represents AWS’s current product offerings and practices as of the date of issue of this document, which are subject to change without notice. Customers are responsible for making their own independent assessment of the information in this document and any use of AWS’s products or services, each of which is provided “as is” without warranty of any kind, whether expressed or implied. This document does not create any warranties, representations, contractual commitments, conditions, or assurances from AWS, its affiliates, suppliers, or licensors. The responsibilities and liabilities of AWS to its customers are controlled by AWS agreements, and this document is not part of, nor does it modify, any agreement between AWS and its customers.

The software included with this paper is licensed under the Apache License, version 2.0 (the "License"). You may not use this file except in compliance with the License. A copy of the License is located at http://aws.amazon.com/apache2.0/ or in the accompanying "license" file. This code is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either expressed or implied. See the License for specific language governing permissions and limitations.