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<article id="post-12314" class="post-12314 post type-post status-publish format-standard has-post-thumbnail hentry category-whats-new tag-assembly tag-comparative-genomics-resource-cgr tag-genome tag-ncbi-datasets">
<img width="1108" height="627" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/10/NCBI_Datasets_Redirect-7.png?resize=1108%2C627&amp;ssl=1" class="attachment-post-thumbnail size-post-thumbnail wp-post-image" alt="NCBI Datasets: Easily Access and Download Sequence Data and Metadata" decoding="async" fetchpriority="high" data-attachment-id="13520" data-permalink="https://ncbiinsights.ncbi.nlm.nih.gov/2023/10/18/ncbi-datasets-access-sequence-data/ncbi_datasets_redirect-7/" data-orig-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/10/NCBI_Datasets_Redirect-7.png?fit=1200%2C627&amp;ssl=1" data-orig-size="1200,627" data-comments-opened="1" data-image-meta="{&quot;aperture&quot;:&quot;0&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;0&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;0&quot;,&quot;iso&quot;:&quot;0&quot;,&quot;shutter_speed&quot;:&quot;0&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;0&quot;}" data-image-title="NCBI_Datasets_Redirect (7)" data-image-description="" data-image-caption="" data-medium-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/10/NCBI_Datasets_Redirect-7.png?fit=300%2C157&amp;ssl=1" data-large-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/10/NCBI_Datasets_Redirect-7.png?fit=1024%2C535&amp;ssl=1" />
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<h1 class="entry-title">NCBI Datasets: Easily Access and Download Sequence Data and Metadata</h1> </header><!-- .entry-header -->
<div class="entry-content">
<h3><i><span data-contrast="auto">Effective June 2024, NCBI Datasets will replace legacy Genome and Assembly web resources</span></i><span data-ccp-props="{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}"> </span></h3>
<p><span data-contrast="none">As part of our ongoing effort to enhance your experience and modernize our services, NCBI will gradually replace the legacy <a href="https://www.ncbi.nlm.nih.gov/genome/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=datasets-sequence-metadata-20221018">Genome</a> and <a href="https://www.ncbi.nlm.nih.gov/assembly/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=datasets-sequence-metadata-20221018">Assembly</a> resources with the newly introduced</span><a href="https://www.ncbi.nlm.nih.gov/datasets/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=datasets-sequence-metadata-20221018"><span data-contrast="none">NCBI Datasets</span></a><span data-contrast="none">resource. NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBI&#8217;s sequence data and metadata.</span><span data-ccp-props="{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}"> </span></p>
<ul>
<li data-leveltext="" data-font="Symbol" data-listid="1" data-list-defn-props="{&quot;335552541&quot;:1,&quot;335559684&quot;:-2,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;&quot;,&quot;469777815&quot;:&quot;multilevel&quot;}" aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span style="font-size: 17px;">The legacy Genome and Assembly web resources will no longer be available after June 2024</span></li>
<li data-leveltext="" data-font="Symbol" data-listid="1" data-list-defn-props="{&quot;335552541&quot;:1,&quot;335559684&quot;:-2,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;&quot;,&quot;469777815&quot;:&quot;multilevel&quot;}" aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span style="font-size: 17px;">There will be no changes to how you access the databases using E-Utilities or EDirect </span></li>
</ul>
<p><span id="more-12314"></span></p>
<h5><b><span data-contrast="auto">Why are we making this change?</span></b><span data-ccp-props="{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}"> </span></h5>
<ul>
<li data-leveltext="" data-font="Symbol" data-listid="3" data-list-defn-props="{&quot;335552541&quot;:1,&quot;335559684&quot;:-2,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}" aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span style="font-size: 17px;">To provide a streamlined experience that integrates genome, organism, and gene information </span></li>
<li data-leveltext="" data-font="Symbol" data-listid="3" data-list-defn-props="{&quot;335552541&quot;:1,&quot;335559684&quot;:-2,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}" aria-setsize="-1" data-aria-posinset="2" data-aria-level="1"><span style="font-size: 17px;">To help you retrieve large datasets that enable big data analyses </span></li>
<li data-leveltext="" data-font="Symbol" data-listid="3" data-list-defn-props="{&quot;335552541&quot;:1,&quot;335559684&quot;:-2,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}" aria-setsize="-1" data-aria-posinset="3" data-aria-level="1"><span style="font-size: 17px;">To deliver data and metadata together and support better reuse and attribution </span></li>
<li data-leveltext="" data-font="Symbol" data-listid="3" data-list-defn-props="{&quot;335552541&quot;:1,&quot;335559684&quot;:-2,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}" aria-setsize="-1" data-aria-posinset="4" data-aria-level="1"><span style="font-size: 17px;">To provide you with a single entry point to genome datasets</span></li>
</ul>
<h5><b><span data-contrast="auto">Features &amp; Benefits of NCBI Datasets</span></b><span data-ccp-props="{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}"> </span></h5>
<ol>
<li><span style="font-size: 17px;"><b>Comprehensive Data</b>: Access assembled genome sequences, annotations, and metadata, including transcripts and proteins from a single webpage </span></li>
<li data-leveltext="%1." data-font="Calibri" data-listid="2" data-list-defn-props="{&quot;335552541&quot;:0,&quot;335559684&quot;:-1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769242&quot;:[65533,0],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;%1.&quot;,&quot;469777815&quot;:&quot;multilevel&quot;}" aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span style="font-size: 17px;"><b>Flexible Search Options</b>: Easily retrieve data using organism names, assembly, WGS, or BioProject accessions </span></li>
<li data-leveltext="%1." data-font="Calibri" data-listid="2" data-list-defn-props="{&quot;335552541&quot;:0,&quot;335559684&quot;:-1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769242&quot;:[65533,0],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;%1.&quot;,&quot;469777815&quot;:&quot;multilevel&quot;}" aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span style="font-size: 17px;"><b>Scalable Data Retrieval</b>: Request data for multiple genomes and file types in a single request, simplifying and expediting the download of large datasets </span></li>
<li data-leveltext="%1." data-font="Calibri" data-listid="2" data-list-defn-props="{&quot;335552541&quot;:0,&quot;335559684&quot;:-1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769242&quot;:[65533,0],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;%1.&quot;,&quot;469777815&quot;:&quot;multilevel&quot;}" aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span style="font-size: 17px;"><b>Well-Documented Metadata</b>: Metadata is sourced from multiple databases, and metadata schemas are thoroughly documented</span></li>
<li data-leveltext="%1." data-font="Calibri" data-listid="2" data-list-defn-props="{&quot;335552541&quot;:0,&quot;335559684&quot;:-1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769242&quot;:[65533,0],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;%1.&quot;,&quot;469777815&quot;:&quot;multilevel&quot;}" aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span style="font-size: 17px;"><b>Interoperable metadata formats</b>: Metadata formats are machine-readable and easily converted to human-readable forms</span></li>
<li data-leveltext="%1." data-font="Calibri" data-listid="2" data-list-defn-props="{&quot;335552541&quot;:0,&quot;335559684&quot;:-1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769242&quot;:[65533,0],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;%1.&quot;,&quot;469777815&quot;:&quot;multilevel&quot;}" aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span style="font-size: 17px;"><b>Taxonomy-Focused Portal</b>: Access genes, genomes, and other NCBI resources through a taxonomy-focused portal</span></li>
<li data-leveltext="%1." data-font="Calibri" data-listid="2" data-list-defn-props="{&quot;335552541&quot;:0,&quot;335559684&quot;:-1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769242&quot;:[65533,0],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;%1.&quot;,&quot;469777815&quot;:&quot;multilevel&quot;}" aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span style="font-size: 17px;"><b>Consistency</b>: Enjoy access to consistent data access across web and programmatic interfaces </span></li>
</ol>
<h5 aria-level="5"><b><span data-contrast="none">Stay up to date</span></b><span data-ccp-props="{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559738&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}"> </span></h5>
<p><span data-contrast="none">NCBI Datasets is part of the</span><a href="https://www.ncbi.nlm.nih.gov/comparative-genomics-resource?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=datasets-sequence-metadata-20221018"><span data-contrast="none">NIH Comparative Genomics Resource (CGR)</span></a>. <span data-contrast="none">CGR facilitates reliable comparative genomics analysesfor all eukaryotic organisms through an NCBI Toolkit and community collaboration.</span><span data-ccp-props="{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559738&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}"> </span></p>
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<h5 aria-level="5"><b><span data-contrast="none">Questions?</span></b><span data-ccp-props="{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559738&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}"> </span></h5>
<p><span data-contrast="none">If you have questions or would like to provide feedback, please reach out to us at </span><a href="mailto:info@ncbi.nlm.nih.gov"><span data-contrast="none">info@ncbi.nlm.nih.gov</span></a><span data-contrast="none">.</span><span data-ccp-props="{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559738&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}"> </span></p>
<p><span data-ccp-props="{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}"> </span></p>
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6 thoughts on &ldquo;<span>NCBI Datasets: Easily Access and Download Sequence Data and Metadata</span>&rdquo; </h2><!-- .comments-title -->
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<img alt='' src='https://secure.gravatar.com/avatar/b28848abd6a57b49d6a2fcfceb9a1648?s=50&#038;d=identicon&#038;r=g' srcset='https://secure.gravatar.com/avatar/b28848abd6a57b49d6a2fcfceb9a1648?s=100&#038;d=identicon&#038;r=g 2x' class='avatar avatar-50 photo' height='50' width='50' decoding='async'/> <b class="fn">Ryan Ward</b> <span class="says">says:</span> </div><!-- .comment-author -->
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2023/10/18/ncbi-datasets-access-sequence-data/#comment-121226"><time datetime="2024-06-14T13:42:30-04:00">June 14, 2024 at 1:42 pm</time></a> </div><!-- .comment-metadata -->
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<p>You can continue to provide both the old assembly resources as well as the new format. Completely deprecating the assembly web resources (and especially command line resources) will break a lot of people&#8217;s workflows.</p>
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2023/10/18/ncbi-datasets-access-sequence-data/#comment-121227"><time datetime="2024-06-14T15:35:06-04:00">June 14, 2024 at 3:35 pm</time></a> </div><!-- .comment-metadata -->
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<p>Thanks for the comment. FTP and access to Assembly data through FTP and the E-Utilities API / EDirect will remain exactly the same as before, so this change should not affect bioinformatic workflows only the web pages.</p>
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2023/10/18/ncbi-datasets-access-sequence-data/#comment-122436"><time datetime="2024-06-27T19:24:45-04:00">June 27, 2024 at 7:24 pm</time></a> </div><!-- .comment-metadata -->
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<p>PLEASE PLEASE PLEASE make it simpler to get a URL to directly command line download one specific file (e.g. assembly .fasta or annotation .gff) that the legacy page provides, rather than the cumbersome URL arguments that generate a .zip file with additional metadata files in multiple subfolders.</p>
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<p>Thank you for your feedback. We will pass it along to the NCBI Datasets Team. Please reach out to our help desk at <a href="mailto:info@ncbi.nlm.nih.gov">info@ncbi.nlm.nih.gov</a>, so we can further assist you.</p>
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<p>is it possible to download genomic gff file in tabular format</p>
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<p>Hello! Thanks for your question. Please contact our help desk so we can assist you: <a href="https://support.nlm.nih.gov/support/create-case/" rel="nofollow ugc">https://support.nlm.nih.gov/support/create-case/</a></p>
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