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@sage-wright
sage-wright committed Dec 5, 2024
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2 changes: 1 addition & 1 deletion main/search/search_index.json
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98 changes: 49 additions & 49 deletions main/sitemap.xml
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14 changes: 11 additions & 3 deletions main/workflows/genomic_characterization/freyja/index.html
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Expand Up @@ -5813,6 +5813,14 @@ <h3 id="freyja_fastq-inputs">Freyja_FASTQ Inputs<a class="headerlink" href="#fre
</tr>
<tr>
<td>freyja_fastq</td>
<td><strong>kraken2_target_organism</strong></td>
<td>String</td>
<td>The organism whose abundance the user wants to check in their reads. This should be a proper taxonomic name recognized by the Kraken database.</td>
<td>"Severe acute respiratory syndrome coronavirus 2"</td>
<td>Optional</td>
</tr>
<tr>
<td>freyja_fastq</td>
<td><strong>ont</strong></td>
<td>Boolean</td>
<td>Indicates if the input data is derived from an ONT instrument.</td>
Expand Down Expand Up @@ -6999,13 +7007,13 @@ <h3 id="freyja_fastq-outputs">Freyja_FASTQ Outputs<a class="headerlink" href="#f
</tr>
<tr>
<td>kraken_sc2</td>
<td>Float</td>
<td>String</td>
<td>Percent of SARS-CoV-2 read data detected using the Kraken2 software</td>
<td>ONT, PE, SE</td>
</tr>
<tr>
<td>kraken_sc2_dehosted</td>
<td>Float</td>
<td>String</td>
<td>Percent of SARS-CoV-2 read data detected using the Kraken2 software after host removal</td>
<td>ONT, PE, SE</td>
</tr>
Expand Down Expand Up @@ -7712,7 +7720,7 @@ <h2 id="references">References<a class="headerlink" href="#references" title="Pe
<span class="md-icon" title="Last update">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1zM12.5 7v5.2l4 2.4-1 1L11 13V7zM11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2z"/></svg>
</span>
<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-11-08</span>
<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-12-05</span>
</span>


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