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<div class="col1">
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<h1 id="download-sra-sequence-data-using">Download SRA sequence data using Amazon Web Services (AWS)</h1>
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<div class="toc">
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<ul>
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<li><a href="#sra-data-in-the-aws-registry-of-">SRA Data in the AWS Registry of Open Data</a><ul>
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<li><a href="#coronaviridae-datasets">Coronaviridae Datasets</a></li>
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<li><a href="#public-data">Public data</a></li>
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<li><a href="#public-usersubmitted-files">Public user-submitted files</a></li>
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</ul>
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</li>
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<li><a href="#accessing-sra-data-in-aws">Accessing SRA Data in AWS</a></li>
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<li><a href="#introduction-for-first-time-user">Introduction for First Time Users</a></li>
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<li><a href="#creating-an-aws-instance">Creating an AWS Instance</a><ul>
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<li><a href="#signin-and-enter-the-amazon-ec2-">Sign-in and Enter the Amazon EC2 Console</a></li>
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<li><a href="#create-an-aws-instance">Create an AWS Instance</a></li>
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<li><a href="#connect-to-the-instance">Connect to the Instance</a></li>
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<li><a href="#terminate-the-instance">Terminate the Instance</a></li>
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</ul>
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</li>
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<li><a href="#the-sra-toolkit-in-aws">The SRA Toolkit in AWS</a><ul>
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<li><a href="#installing-the-sra-toolkit-in-yo">Installing The SRA Toolkit in your instance</a></li>
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<li><a href="#using-the-sra-toolkit-in-aws">Using the SRA Toolkit in AWS</a></li>
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</ul>
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</li>
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<li><a href="#youtube-video-tutorial-setting-u">Youtube Video Tutorial - Setting up AWS - demo</a></li>
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<li><a href="#engage">Engage</a></li>
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</ul>
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</div>
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<h2 id="sra-data-in-the-aws-registry-of-">SRA Data in the AWS Registry of Open Data</h2>
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<p><a target="_blank" title="NCB-coronavirus data available on AWS, new window" href="https://aws.amazon.com/blogs/publicsector/taking-covid-strides-national-center-biotechnology-information-coronavirus-genomic-data-available-aws">Amazon Web Services publicly hosts SRA data<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a>
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through
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the <a target="_blank" title="Registry of Open Data, new window" href="https://aws.amazon.com/opendata/open-data-sponsorship-program">Registry of Open Data<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a>.
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SRA has several datasets in the AWS Registry of
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Open Data, all of which can be accessed freely, without charge, through either an HTTPS or S3 URL. One dataset contains public SRA
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data in the originally submitted format from select high value and newly-released studies. The second dataset acts as a centralized repository of
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SARS-CoV-2 related sequences submitted to NCBI. Included are both the original files submitted by the principal investigator as well as SRA-processed
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sequences (including normalized sequence files and SRA
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<a title="SRA alighned read format" href="sra/docs/sra-aligned-read-format/">aligned read format</a> files) that require the
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<a title="SRA Toolkit" href="https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit">SRA Toolkit</a> for analysis. This dataset also includes
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metadata <a title="Search in Athena" href="/sra/docs/sra-athena/">searchable in AWS Athena</a>
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by BLAST result, taxonomic analysis, and more, to allow rapid discovery of the most relevant data to your research. </p>
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<h3 id="coronaviridae-datasets"><a target="_blank" title="Coronaviridae Datasets" href="https://registry.opendata.aws/ncbi-covid-19/">Coronaviridae Datasets<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a></h3>
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<ul>
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<li><strong>Runs</strong> directory contains normalized sequence data, accessible in multiple formats (fastq, sam, fasta) via the SRA Toolkit and organized by Run accession. </li>
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<li><strong>sra-src</strong> directory contains the submitted sequence files in their original format, organized by Run accession. </li>
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<li><strong>VCF</strong> directory contains SRA generated VCF files, organized by Run accession. </li>
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</ul>
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<p>AWS CLI Access (No AWS account required): </p>
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<p><code>aws s3 ls s3://sra-pub-sars-cov2/ --no-sign-request</code> </p>
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<h3 id="public-data"><a target="_blank" title="Public data" href="https://registry.opendata.aws/ncbi-sra/">Public data<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a></h3>
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<ul>
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<li>Contains all public SRA Runs organized by Run accession. </li>
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</ul>
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<p>AWS CLI Access (No AWS account required): </p>
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<p><code>aws s3 ls s3://sra-pub-run-odp/ --no-sign-request</code> </p>
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<h3 id="public-usersubmitted-files"><a target="_blank" title="Public submitted files" href="https://registry.opendata.aws/ncbi-sra/">Public user-submitted files<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a></h3>
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<ul>
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<li>Contains submitted sequence files in their original format, organized by Run accession. </li>
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</ul>
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<p>AWS CLI Access (No AWS account required): </p>
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<p><code>aws s3 ls s3://sra-pub-src-2/ --no-sign-request</code> </p>
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<h2 id="accessing-sra-data-in-aws">Accessing SRA Data in AWS</h2>
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<p>If you know your Run accessions of interest you can access the data several ways.
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To download files from the <a target="_blank" title="Amazon AWS Console, new window" href="https://aws.amazon.com/">AWS Console<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a> using a
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browser, visit the HTTPS URL for the Coronaviridae dataset, Public SRA data, or Public user-submitted files respectively: </p>
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<ul>
|
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<li>https://s3.console.aws.amazon.com/s3/buckets/sra-pub-sars-cov2/ </li>
|
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<li>https://s3.console.aws.amazon.com/s3/buckets/sra-pub-run-odp/ </li>
|
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<li>https://s3.console.aws.amazon.com/s3/buckets/sra-pub-src-2/ </li>
|
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</ul>
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|
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<p>From there you can navigate the directory structure using the provided graphical interface and you can
|
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search a given directory for your accession of interest using the provided search box near the top of the page.
|
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Once you have navigated to a specific file of interest you can click the <strong>Object URL</strong> link or use the <strong>Object actions</strong>
|
|
button to copy the file to your own S3 bucket or download a copy to local storage. </p>
|
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|
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<p>To access files from <em>within</em> AWS, e.g. from an EC2 instance, you can use the
|
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<a target="_blank" title="AWS CLI, new window" href="https://aws.amazon.com/cli/">AWS CLI<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a>
|
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to perform an S3 copy or sync, using a command like this: </p>
|
|
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|
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<p><code>aws s3 cp s3://sra-pub-sars-cov2/README.txt $USER/$HOME/README.txt</code> </p>
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|
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<p>These data can also be accessed using various other
|
|
<a target="_blank" title="AWS tools and libraries, new window" href="https://docs.aws.amazon.com/AmazonS3/latest/dev/UsingAWSSDK.html">tools and libraries<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a>.
|
|
Access to files in the
|
|
<a target="_blank" title="AWS Registry of Open Data, new window" href="https://aws.amazon.com/opendata/public-datasets/">AWS Registry of Open Data<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a>
|
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is free. This is true whether you use the HTTPS or S3 URL. For S3 URLs, the transfer is free even if it crosses an AWS region boundary; there is no
|
|
<a target="_blank" title="inter-regional data transfer fee, new window" href="https://aws.amazon.com/s3/pricing/">inter-regional data transfer fee<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a>. </p>
|
|
|
|
|
|
<p>If you don't know the Run accessions you are interested in, you can start by searching in the
|
|
<a title="SRA Run Selector" href="/Traces/study/">SRA Run Selector</a>,<br />
|
|
<a target="_blank" title="AWS Athena - Youtube" href="https://www.youtube.com/watch?v=_F4FhcDWSJg">AWS Athena<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a>, or
|
|
<a title="SRA Entrez" href="/sra">SRA Entrez</a>.<br />
|
|
A full list of Coronaviridae-containing SRA runs as detected with NCBI's kmer analysis tool is available here: <a title="SRA FTP: full list of Coronaviridae-containing SRA runs" href="https://ftp.ncbi.nlm.nih.gov/sra/reports/AccList/">ftp://ftp.ncbi.nlm.nih.gov/sra/reports/AccList/ </a>. </p>
|
|
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|
|
<h2 id="introduction-for-first-time-user">Introduction for First Time Users</h2>
|
|
|
|
|
|
<p><strong>Amazon Elastic Compute Cloud (EC2)</strong> is the Amazon Web Service you use to create and run virtual machines in the cloud.
|
|
AWS calls these virtual machines 'instances'.
|
|
You will need to install your bioinformatics tools for data analysis and the SRA Toolkit for accessing the SRA data. </p>
|
|
|
|
|
|
<h2 id="creating-an-aws-instance">Creating an AWS Instance</h2>
|
|
|
|
|
|
<p><img src="/core/assets/sra/images/znak.png" alt="Exclamation point" height="20" /> Users will need to address accounts on their own. <br />
|
|
Please work with your organization for credential and billing questions. If using a personal account, this guide attempts to stay within <strong>AWS Free Tier</strong> for users who are still eligible. </p>
|
|
|
|
|
|
<p><img src="/core/assets/sra/images/znak.png" alt="Exclamation point" height="20" /> Users of this guide are expected to have experience using a Unix command-line interface. </p>
|
|
|
|
|
|
<h3 id="signin-and-enter-the-amazon-ec2-">Sign-in and Enter the Amazon EC2 Console</h3>
|
|
|
|
|
|
<p>Sign-in using your AWS account: <a target="_blank" title="Amazon AWS Console, new window" href="https://aws.amazon.com/">Amazon AWS Console<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a>. </p>
|
|
|
|
|
|
<h3 id="create-an-aws-instance">Create an AWS Instance</h3>
|
|
|
|
|
|
<p>Please follow this <a target="_blank" title="Amazon AWS guide, new window" href="https://docs.aws.amazon.com/efs/latest/ug/gs-step-one-create-ec2-resources.html">Amazon step-by-step guide<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a>
|
|
that will help you launch a Linux virtual machine on Amazon EC2 within Amazon AWS Free Tier.<br />
|
|
Please make sure to create your EC2 instance in the <strong>US East (N. Virginia) us-east-1 region</strong>. </p>
|
|
|
|
|
|
<h3 id="connect-to-the-instance">Connect to the Instance</h3>
|
|
|
|
|
|
<p>Use either a Unix/OSX terminal or your preferred ssh application to connect the same as the Amazon tutorial linked above.
|
|
- This AMI username is <strong>ec2-user</strong>. </p>
|
|
|
|
|
|
<h3 id="terminate-the-instance">Terminate the Instance</h3>
|
|
|
|
|
|
<ul>
|
|
<li>Remember to terminate the EC2 instance from the AWS console when you have finished using it. If you do not terminate the instance, charges can be generated on your account even when no users are connected. </li>
|
|
<li>Data stored on the EC2 instance will be deleted when the instance is terminated. Users will likely want to have stable s3 storage to store results from their work. </li>
|
|
</ul>
|
|
|
|
|
|
<h2 id="the-sra-toolkit-in-aws">The SRA Toolkit in AWS</h2>
|
|
|
|
|
|
<h3 id="installing-the-sra-toolkit-in-yo">Installing The SRA Toolkit in your instance</h3>
|
|
|
|
|
|
<p>Once you connected, you will be able to work in Unix-like command line environment where you can install and configure the SRA Toolkit. </p>
|
|
|
|
|
|
<ul>
|
|
<li><a target="_blank" title="Installing the SRA Toolkit" href="https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit">Installing the SRA Toolkit</a> </li>
|
|
</ul>
|
|
|
|
|
|
<h3 id="using-the-sra-toolkit-in-aws">Using the SRA Toolkit in AWS</h3>
|
|
|
|
|
|
<ul>
|
|
<li>For downloading public SRA data from our cloud buckets to your cloud storage you can use the SRA Toolkit utilities as described in the <a title="SRA Download Guide" href="/sra/docs/sradownload">SRA Download Guide</a> </li>
|
|
<li>For downloading dbGAP data from our cloud buckets to your cloud storage you need to use <strong>jwt.cart</strong> file as descibed in the <a title="Downloading dbGaP data with JWT" href="/sra/docs/sra-dbGAP-cloud-download">Downloading dbGaP data with JWT</a> </li>
|
|
</ul>
|
|
|
|
|
|
<p><span class="warning-message"><img src="/core/assets/sra/images/tack.png" alt="Tack" height="30" />Don't forget to STOP your instance after you finished your work! </span> </p>
|
|
|
|
|
|
<h2 id="youtube-video-tutorial-setting-u">Youtube Video Tutorial - Setting up AWS - demo</h2>
|
|
|
|
|
|
<ul>
|
|
<li><a title="Setting up AWS demo" href="https://www.youtube.com/watch?v=rjjrHnZfymU">Setting up AWS demo</a> </li>
|
|
</ul>
|
|
|
|
|
|
<iframe src="https://www.youtube.com/embed/rjjrHnZfymU" width="647" height="364" title="How to Access SRA Data with Amazon Web Services" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen=""></iframe>
|
|
|
|
|
|
<h2 id="engage">Engage</h2>
|
|
|
|
|
|
<p>NCBI wants your feedback on SRA in the Cloud. Contact <a href="mailto:sra@ncbi.nlm.nih.gov?subject=SRA%20question&body=Dear%20SRA%20staff">sra@ncbi.nlm.nih.gov</a> with questions or if you would like to provide input on new functionality.</p>
|
|
|
|
|
|
</div>
|
|
<!--/.col1-->
|
|
<div class="col2">
|
|
<div id="shared-content-1">
|
|
<h2 data-heading="h2" data-no-toc="true">Getting Started</h2>
|
|
<ul>
|
|
<li><a title="SRA Getting Started" href="/sra/docs/">Getting Started</a> </li>
|
|
</ul>
|
|
<h2 data-heading="h2" data-no-toc="true">Cloud Quick Start</h2>
|
|
<ul>
|
|
<li><a title="SRA Cloud getting started" href="/sra/docs/sra-cloud">Cloud Introduction</a> </li>
|
|
<li><a target="_blank" title="SRA on YouTube: Tutorials" href="https://www.youtube.com/playlist?list=PL7dF9e2qSW0ZZci13mHSKZYis3MV4Mdoa">YouTube Tutorials</a> </li>
|
|
<li><a title="GCP SARS-CoV-2 Public Dataset Guide" href="/sra/docs/gcp-pdp-guide">GCP SARS-CoV-2 Public Dataset Guide</a> </li>
|
|
<li><a title="SRA Cloud Access Costs" href="/sra/docs/sra-cloud-access-costs">SRA Cloud Access Costs</a> </li>
|
|
</ul>
|
|
<h2 data-heading="h2" data-no-toc="true">Setting Up</h2>
|
|
<ul>
|
|
<li><a title="SRA Google Cloud" href="/sra/docs/SRA-Google-Cloud">Set up Google Cloud</a> </li>
|
|
<li><a title="SRA Amazon Cloud" href="/sra/docs/sra-aws-download/">Set up Amazon Cloud</a> </li>
|
|
<li><a title="SRA in BigQuery" href="/sra/docs/sra-bigquery">Set up BigQuery</a> </li>
|
|
<li><a title="SRA in Athena" href="/sra/docs/sra-athena">Set up Athena</a> </li>
|
|
</ul>
|
|
<h2 data-heading="h2" data-no-toc="true">Cloud Data Access</h2>
|
|
<ul>
|
|
<li><a title="Download SRA sequences from Entrez search results" href="/sra/docs/sradownload">Download Guide</a> </li>
|
|
<li><a title="Data Delivery to cloud bucket" href="/sra/docs/data-delivery">Cloud Data Delivery Service</a> </li>
|
|
</ul>
|
|
<h2 data-heading="h2" data-no-toc="true">Accessing dbGAP</h2>
|
|
<ul>
|
|
<li><a title="Download dbGAP from cloud" href="/sra/docs/sra-dbGAP-cloud-download">Download dbGAP with JWT</a> </li>
|
|
</ul>
|
|
<h2 data-heading="h2" data-no-toc="true">Search</h2>
|
|
<ul>
|
|
<li><a title="SRA cloud-based search" href="/sra/docs/sra-cloud-based-examples">Cloud-based Search</a> </li>
|
|
<li><a title="SRA in BigQuery" href="/sra/docs/sra-bigquery-examples">Search in BigQuery</a> </li>
|
|
<li><a title="SRA in Athena" href="/sra/docs/sra-athena-examples">Search in Athena</a> </li>
|
|
</ul>
|
|
<h2 data-heading="h2" data-no-toc="true">SRA Analysis</h2>
|
|
<ul>
|
|
<li><a title="SRA Aligned Read Format" href="/sra/docs/sra-aligned-read-format">SRA Aligned Read Format</a> </li>
|
|
<li><a title="SRA SARS-CoV-2 Detection Tool" href="/sra/docs/sra-detection-tool">SARS-CoV-2 Detection Tool</a> </li>
|
|
<li><a title="SARS-CoV-2 Variant Calling" href="/sra/docs/sars-cov-2-variant-calling">SARS-CoV-2 Variant Calling</a> </li>
|
|
<li><a title="SRA Taxonomy Analysis Tool" href="/sra/docs/sra-taxonomy-analysis-tool">SRA Taxonomy Analysis Tool</a> </li>
|
|
</ul>
|
|
<h2 data-heading="h2" data-no-toc="true">SRA Data Formats</h2>
|
|
<ul>
|
|
<li><a title="SRA Data Formats" href="/sra/docs/sra-data-formats">SRA Data Formats</a> </li>
|
|
<li><a title="Data Format FAQ" href="/sra/docs/data-format-faq">Data Format FAQ</a> </li>
|
|
</ul>
|
|
</div>
|
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</div>
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<!--/.col2-->
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