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HTML
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<div class="search"><form method="get" action="/sra/"><div class="search_form"><label for="database" class="offscreen_noflow">Search database</label><select id="database"><optgroup label="Recent"><option value="sra" selected="selected">SRA</option><option value="nuccore">Nucleotide</option><option value="books">Books</option><option value="pubmed" class="last">PubMed</option></optgroup><optgroup label="All"><option value="gquery">All Databases</option><option value="assembly">Assembly</option><option value="biocollections">Biocollections</option><option value="bioproject">BioProject</option><option value="biosample">BioSample</option><option value="books">Books</option><option value="clinvar">ClinVar</option><option value="cdd">Conserved Domains</option><option value="gap">dbGaP</option><option value="dbvar">dbVar</option><option value="gene">Gene</option><option value="genome">Genome</option><option value="gds">GEO DataSets</option><option value="geoprofiles">GEO Profiles</option><option value="gtr">GTR</option><option value="ipg">Identical Protein Groups</option><option value="medgen">MedGen</option><option value="mesh">MeSH</option><option value="nlmcatalog">NLM Catalog</option><option value="nuccore">Nucleotide</option><option value="omim">OMIM</option><option value="pmc">PMC</option><option value="protein">Protein</option><option value="proteinclusters">Protein Clusters</option><option value="protfam">Protein Family Models</option><option value="pcassay">PubChem BioAssay</option><option value="pccompound">PubChem Compound</option><option value="pcsubstance">PubChem Substance</option><option value="pubmed">PubMed</option><option value="snp">SNP</option><option value="sra">SRA</option><option value="structure">Structure</option><option value="taxonomy">Taxonomy</option><option value="toolkit">ToolKit</option><option value="toolkitall">ToolKitAll</option><option value="toolkitbookgh">ToolKitBookgh</option></optgroup></select><div class="nowrap"><label for="term" class="offscreen_noflow" accesskey="/">Search term</label><div class="nowrap"><input type="text" name="term" id="term" title="Search SRA" value="" class="jig-ncbiclearbutton jig-ncbiautocomplete" data-jigconfig="isEnabled:false,disableUrl:'NcbiSearchBarAutoComplCtrl'" autocomplete="off" data-sbconfig="ds:'no',pjs:'no',afs:'yes'" /></div><button id="search" type="submit" class="button_search nowrap" cmd="go">Search</button></div></div></form><ul class=" inline_list searchlinks"><li>
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<li>
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<a title="Getting Started" href="/sra/docs/">Getting Started</a></li>
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<a title="SRA Submission Quick Start" href="/sra/docs/submit">Submission Quick Start</a></li>
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<a title="SRA Search and Download Guide" href="/sra/docs/sradownload">Search and Download</a>
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<a title="How to use SRA in the cloud" href="/sra/docs/sra-cloud">SRA in the Cloud</a>
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<a title="Archive Documentation" href="/sra/docs/sra-data-storage-model/">Archive Documentation</a>
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<ul>
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<li><a title="Data Storage Model" href="/sra/docs/sra-data-storage-model/">Data Storage Model</a></li>
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<li><a title="Root Cause Analysis: Summary and Report" href="/sra/docs/rca/">Root Cause Analysis: Summary and Report</a></li>
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<div class="container">
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<div id="maincontent" class="content col twelve_col last">
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<div class="col1">
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<h1 id="get-started-in-athena">Get Started in Athena</h1>
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<div class="toc">
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<ul>
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<li><a href="#setup">Setup</a></li>
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<li><a href="#the-table-s3-locations">The table S3 locations</a><ul>
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<li><a href="#for-all-sra-metadata">For all SRA metadata</a></li>
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<li><a href="#for-the-coronaviridae-specific-d">For the Coronaviridae specific dataset</a></li>
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</ul>
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</li>
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<li><a href="#access-methods">Access methods</a></li>
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<li><a href="#payment">Payment</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="setup">Setup</h2>
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<p>To get started with Athena, you will need an Amazon AWS account. Please follow the
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<a target="_blank" title="AWS-provided tutorial" href="https://docs.aws.amazon.com/athena/latest/ug/getting-started.html">AWS-provided tutorial</a> to become familiar with: </p>
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<ul>
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<li><a title="Creating S3 buckets" href="https://docs.aws.amazon.com/AmazonS3/latest/gsg/CreatingABucket.html">Creating S3 buckets</a> for saving your results </li>
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<li><a title="Creating databases" href="https://docs.aws.amazon.com/athena/latest/ug/getting-started.html#step-1-create-a-database">Creating databases</a> </li>
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<li><a title="Creating tables" href="https://docs.aws.amazon.com/athena/latest/ug/getting-started.html#step-2-create-a-table">Creating tables</a> </li>
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<li><a title="Querying tables" href="https://docs.aws.amazon.com/athena/latest/ug/getting-started.html#step-3-query-data">Querying tables</a> </li>
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</ul>
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<p>Please make sure you create your bucket for saving results in the <strong>US-east-1</strong> region.<br />
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We recommend using <a target="_blank" title="AWS Glue" href="https://docs.aws.amazon.com/athena/latest/ug/creating-tables.html#creating-tables-how-to">AWS Glue</a> to create the tables from the bucket.
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In order to create the tables, you need to include the S3 location of the metadata. SRA provides data in two different locations: </p>
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<ol>
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<li>Coronaviridae dataset in the AWS Public Dataset Program: s3://sra-pub-sars-cov2-metadata-us-east-1/ </li>
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<li>Entire SRA metadata: s3://sra-pub-metadata-us-east-1 </li>
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</ol>
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<p><a title="AWS Glue charge" href="https://aws.amazon.com/glue/pricing/">AWS Glue does have a small charge</a> associated with it, based on the number of tables in the catalog and the amount
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of time it takes to run the crawler to find all the datasets. The crawler charge will generally be less than $1.<br />
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With the AWS Glue Data Catalog, you can store up to a million objects for free. An object in the AWS Glue Data Catalog is a table, table version,
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partition, or database. The first million access requests to the AWS Glue Data Catalog per month are free.<br />
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Alternatively, you can opt to <a title="Create a database in AWS" href="https://docs.aws.amazon.com/athena/latest/ug/creating-databases.html">manually create a database</a> yourself
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and <a title="Add the tables in AWS" href="https://docs.aws.amazon.com/athena/latest/ug/creating-tables.html#to-create-a-table-using-the-wizard">add the tables</a>.<br />
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You can find the table definitions here: <a title="SRA Cloud Based Table Definitions" href="/sra/docs/sra-cloud-based-examples">SRA Cloud Based Table Definitions</a>. </p>
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<h2 id="the-table-s3-locations">The table S3 locations</h2>
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<p>These data can be accessed using the command line interface with the <code>--no-sign-request</code> option, see examples below. </p>
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<h3 id="for-all-sra-metadata">For all SRA metadata</h3>
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<ul>
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<li>metadata: <code>aws s3 ls s3://sra-pub-metadata-us-east-1/sra/metadata/ --no-sign-request</code> </li>
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<li>taxonomy analysis: <code>aws s3 ls s3://sra-pub-metadata-us-east-1/sra_tax_analysis_tool/tax_analysis/ --no-sign-request</code> </li>
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<li>tax analysis info: <code>aws s3 ls s3://sra-pub-metadata-us-east-1/sra_tax_analysis_tool/tax_analysis_info/ --no-sign-request</code> </li>
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<li>taxonomy: <code>aws s3 ls s3://sra-pub-metadata-us-east-1/sra_tax_analysis_tool/taxonomy/ --no-sign-request</code> </li>
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<li>kmer: <code>aws s3 ls s3://sra-pub-metadata-us-east-1/sra_tax_analysis_tool/kmer/ --no-sign-request</code> </li>
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</ul>
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<h3 id="for-the-coronaviridae-specific-d">For the Coronaviridae specific dataset</h3>
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<ul>
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<li>annotated variations: <code>aws s3 ls s3://sra-pub-sars-cov2-metadata-us-east-1/annotated_variations/ --no-sign-request</code> </li>
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</ul>
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<h2 id="access-methods">Access methods</h2>
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<p>We recommend first using the Athena query editor to become familiar with writing queries before attempting to use the command line tools or client libraries. </p>
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<p>Athena can be accessed through a web browser query editor:<br />
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<a title="Athena web browser query editor" href="https://console.aws.amazon.com/athena/">https://console.aws.amazon.com/athena/</a>. <br />
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</p>
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<p>Athena client library documentation is also available for reference if you plan to access it through the AWS CLI or one of the supported SDKs:<br />
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<a title="AWS CLI or one of the supported SDKs" href="https://docs.aws.amazon.com/cli/latest/reference/athena/">https://docs.aws.amazon.com/cli/latest/reference/athena/</a>.<br />
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</p>
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<p>AWS command line tools can be downloaded and set up from here:<br />
|
||
<a title="AWS command line tools" href="https://docs.aws.amazon.com/cli/latest/userguide/cli-chap-welcome.html">https://docs.aws.amazon.com/cli/latest/userguide/cli-chap-welcome.html</a>.<br />
|
||
</p>
|
||
|
||
|
||
<p>Please see <a title="the AWS documentation" href="https://docs.aws.amazon.com/athena/latest/ug/accessing-Athena.html">the AWS documentation</a> for more information on these options. </p>
|
||
|
||
|
||
<h2 id="payment">Payment</h2>
|
||
|
||
|
||
<p>The user pays to run queries against public data sets and for storage of results in S3.
|
||
We recommend all users review the payment requirements for
|
||
<a title="on-demand queries from Athena" href="https://aws.amazon.com/athena/pricing/">on-demand queries from Athena</a>. </p>
|
||
|
||
|
||
<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>
|
||
|
||
|
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</div>
|
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<!--/.col1-->
|
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<div class="col2">
|
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<div id="shared-content-1">
|
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<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>
|
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</ul>
|
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|
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