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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="sra-taxonomy-analysis-tool">SRA Taxonomy Analysis Tool</h1>
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<h2 id="overview">Overview</h2>
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<p>The NCBI SRA Taxonomy Analysis Tool (STAT) calculates the taxonomic distribution of reads from next generation sequencing runs. This analysis maps individual
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sequencing reads to a taxonomic hierarchy and reports the taxonomic composition of reads within a sequencing run. </p>
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<h2 id="method">Method</h2>
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<p>STAT maps sequencing reads to a taxonomic hierarchy using a two-step strategy based on exact query read matches
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to precomputed k-mer dictionary databases. In the first pass, a small, "coarse" reference dictionary database is
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used to identify organisms matching a read set. In the second pass, organism-specific slices from a "fine"
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reference dictionary database are used to compute distribution of reads between identified taxonomy classes (species and higher order taxonomy nodes).
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When multiple tax nodes are mapped for single spot, we use the lowest non-ambiguous mapping. </p>
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<p>STAT k-mer dictionaries are built using an iterative minhash based approach against reference genomic databases.
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For every fixed segment length of incoming reference nucleotide sequence, k-mer representing this
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segment are selected based on minimum fvn1 hash function. Several strategies were used to enhance the
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specificity and accuracy of STAT results. Low complexity k-mers composed of >50% homo-polymer or dinucleotide repeats
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(e.g. AAAAAA or ACACACACACA) were filtered from dictionaries, and discrete k-mers belonging to multiple taxonomic references
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were "merged" at the lowest common taxonomic node shared between references. Finally, the specificity of representative
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k-mers was determined by searching against the source reference genomic database. When representative k-mers were found
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in multiple taxonomic references nodes,
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they were merged at the lowest common taxonomic node as above. </p>
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<h2 id="genome-references">Genome references</h2>
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<p>The NCBI <a target="_blank" title="RefSeq" href="/refseq/">RefSeq genomic database</a> was
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supplemented with the viral genome set from nt and used as the source for k-mer creation in both "coarse" and "fine" sets. </p>
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<h2 id="taxonomy-hierarchy">Taxonomy hierarchy</h2>
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<p>Reference sequences were mapped to the taxonomy hierarchy using the NCBI <a target="_blank" title="Taxonomy" href="/taxonomy/">Taxonomy database</a>.
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The database contained 2,383,364 taxonomy nodes in March 2020. </p>
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<h2 id="segment-sizes-and-kmer-selection">Segment sizes and K-mer selection</h2>
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<p>K-mer dictionaries were built by computationally slicing reference genomes into
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sequential segments and selecting 32-mers to represent each segment. The "coarse"
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k-mer dictionary uses variable segment lengths proportional to genomes size and ranging from 200-8000 nt.
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The "fine" k-mer dictionary uses a constant 64 nt segment length for all genomes; for 32-mer index it gives us 32x reduction in
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space with the assumption that we have at least one error-free 64-mer for every spot. </p>
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<h2 id="frequently-asked-questions">Frequently Asked Questions</h2>
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||
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||
<h3 id="are-all-sra-runs-analyzed-using-">Are all SRA Runs analyzed using the course and fine databases?</h3>
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<p>Yes, each public run is analyzed with both databases. </p>
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<h3 id="can-i-get-the-software">Can I get the software?</h3>
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<p>Yes. At <a target="_blank" title="Github taxonomy" href="https://github.com/ncbi/ngs-tools/tree/tax/tools/tax">github</a> </p>
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||
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||
<div class="gray-box">
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||
<span class="code">
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git clone https://github.com/ncbi/ncbi-vdb.git<br />
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git clone https://github.com/ncbi/sra-tools.git<br />
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git clone https://github.com/ncbi/ngs-tools.git --branch tax<br />
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<br />
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cd ncbi-vdb<br />
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./configure<br />
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make<br />
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||
<br />
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cd ../sra-tools<br />
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./configure<br />
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make -C ngs<br />
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<br />
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cd ../ngs-tools<br />
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./configure<br />
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make -C tools/tax
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</span></div>
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<p>And in <code>./examples</code> folder you can find helper <code>*.sh</code> scripts. </p>
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<h3 id="how-can-i-cite-you">How can I cite you?</h3>
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<p>The publication associated with this tool is available here: <a target="_blank" title="Taxonomy Analysis Tool preprint" href="https://pubmed.ncbi.nlm.nih.gov/34544477/">https://pubmed.ncbi.nlm.nih.gov/34544477/</a> </p>
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<h2 id="contact-sra">Contact SRA</h2>
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<p>Contact SRA staff for assistance at <a href="mailto:sra@ncbi.nlm.nih.gov?subject=SRA%20question&body=Dear%20SRA%20staff">sra@ncbi.nlm.nih.gov</a> </p>
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<h2 data-heading="h2" data-no-toc="true">Getting Started</h2>
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<ul>
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<li><a title="SRA Getting Started" href="/sra/docs/">Getting Started</a> </li>
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</ul>
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<h2 data-heading="h2" data-no-toc="true">Cloud Quick Start</h2>
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<ul>
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<li><a title="SRA Cloud getting started" href="/sra/docs/sra-cloud">Cloud Introduction</a> </li>
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<li><a target="_blank" title="SRA on YouTube: Tutorials" href="https://www.youtube.com/playlist?list=PL7dF9e2qSW0ZZci13mHSKZYis3MV4Mdoa">YouTube Tutorials</a> </li>
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<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>
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<li><a title="SRA Cloud Access Costs" href="/sra/docs/sra-cloud-access-costs">SRA Cloud Access Costs</a> </li>
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</ul>
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<h2 data-heading="h2" data-no-toc="true">Setting Up</h2>
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<ul>
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||
<li><a title="SRA Google Cloud" href="/sra/docs/SRA-Google-Cloud">Set up Google Cloud</a> </li>
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<li><a title="SRA Amazon Cloud" href="/sra/docs/sra-aws-download/">Set up Amazon Cloud</a> </li>
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<li><a title="SRA in BigQuery" href="/sra/docs/sra-bigquery">Set up BigQuery</a> </li>
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<li><a title="SRA in Athena" href="/sra/docs/sra-athena">Set up Athena</a> </li>
|
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</ul>
|
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<h2 data-heading="h2" data-no-toc="true">Cloud Data Access</h2>
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<li><a title="Download SRA sequences from Entrez search results" href="/sra/docs/sradownload">Download Guide</a> </li>
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<li><a title="Download dbGAP from cloud" href="/sra/docs/sra-dbGAP-cloud-download">Download dbGAP with JWT</a> </li>
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<h2 data-heading="h2" data-no-toc="true">Search</h2>
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<h2 data-heading="h2" data-no-toc="true">SRA Analysis</h2>
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<li><a title="SRA Aligned Read Format" href="/sra/docs/sra-aligned-read-format">SRA Aligned Read Format</a> </li>
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<li><a title="SRA SARS-CoV-2 Detection Tool" href="/sra/docs/sra-detection-tool">SARS-CoV-2 Detection Tool</a> </li>
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<li><a title="SRA Taxonomy Analysis Tool" href="/sra/docs/sra-taxonomy-analysis-tool">SRA Taxonomy Analysis Tool</a> </li>
|
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|
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<h2 data-heading="h2" data-no-toc="true">SRA Data Formats</h2>
|
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<li><a title="SRA Data Formats" href="/sra/docs/sra-data-formats">SRA Data Formats</a> </li>
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</li>
|
||
<li>
|
||
<a class="text-white" href="https://www.hhs.gov/">HHS</a>
|
||
</li>
|
||
<li>
|
||
<a class="text-white" href="https://www.usa.gov/">USA.gov</a>
|
||
</li>
|
||
</ul>
|
||
</nav>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<script type="text/javascript" src="/portal/portal3rc.fcgi/rlib/js/InstrumentOmnitureBaseJS/InstrumentNCBIConfigJS/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js?v=1"> </script>
|
||
<script type="text/javascript" src="/portal/portal3rc.fcgi/static/js/hfjs2.js"> </script>
|
||
</div>
|
||
</div>
|
||
<!--/.footer-->
|
||
<p class="last-updated small">Last updated: 2022-06-24T17:41:43Z</p>
|
||
</div>
|
||
<!--/.page-->
|
||
</div>
|
||
<!--/.wrap-->
|
||
<span class="PAFAppResources"></span>
|
||
|
||
|
||
</div><!-- /.twelve_col -->
|
||
</div>
|
||
<!-- /.grid -->
|
||
|
||
|
||
|
||
<!-- usually for JS scripts at page bottom -->
|
||
<span class="pagefixtures"></span>
|
||
|
||
|
||
<!-- CE8B5AF87C7FFCB1_0191SID /projects/staticsites/SraDocs@1.5 portal107 v4.1.r689238 Tue, Oct 22 2024 16:10:51 -->
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<span id="portal-csrf-token" style="display:none" data-token="CE8B5AF87C7FFCB1_0191SID"></span>
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||
|
||
<script type="text/javascript" src="//static.pubmed.gov/portal/portal3rc.fcgi/4217302/js/3879255/4121861/4082503/4217304/4087685.js" snapshot="sra"></script></body>
|
||
</html>
|
||
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