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<h1 id="datasets-downloads-for-pathogen-">Datasets downloads for Pathogen Detection isolates <a href="/pathogens/pathogens_help/#isolates-browser"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h1>
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<p>The <a href="/datasets/docs/v2/download-and-install/">Datasets command-line tool</a> allows you to download large amounts of data using the "<a href="/datasets/docs/v2/how-tos/genomes/large-download/">dehydrated download</a>" feature. To download large numbers of assemblies using this tool first you need to <a href="/datasets/docs/v2/download-and-install/">Install datasets</a>.</p>
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<p>Here's an example of how to use this feature to download all 68,000+ <em>Listeria monocytogenes</em> genomes available in Pathogen Detection and included in GenBank. </p>
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<h2 id="1-select-the-isolates-you-want-t">1. Select the isolates you want to download using the Isolates Browser</h2>
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<p>In this example we will download all <em>Listeria monocytogenes</em> genomes using the query <a href="/pathogens/isolates#taxgroup_name:%22Listeria%20monocytogenes%22">taxgroup_name:"Listeria monocytogenes"</a> in the <a href="/pathogens/isolates#taxgroup_name:%22Listeria%20monocytogenes%22">Isolates Browser</a> and click on the Download link.</p>
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<h3 id="3-download-a-dehydrated-data-pac">3. Download a "dehydrated data package" using the <a href="/datasets/docs/v2/download-and-install/">datasets CLI</a>.</h3>
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<p>Here we will download the assembly, annotation GFF3 file, and annotated proteins</p>
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<pre><code>datasets download genome accession --dehydrated --inputfile accessions.txt --include genome,gff3,protein
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</code></pre>
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<h3 id="4-unzip-the-downloaded-zip-archi">4. Unzip the downloaded zip archive to a directory</h3>
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<pre><code>unzip ncbi_dataset.zip -d listeria_genomes
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</code></pre>
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<h3 id="5-rehydrate-the-extracted-zip-ar">5. "Rehydrate" the extracted zip archive to retrieve the data</h3>
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<pre><code>datasets rehydrate --directory listeria_genomes
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</code></pre>
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<p>For more information on the datasets CLI see the <a href="/datasets/docs/v2/download-and-install/">datasets CLI documentation</a>.</p>
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