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shenwei356 committed Oct 19, 2024
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22 changes: 16 additions & 6 deletions faqs/index.html
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<meta name="description" content="Table of contents Table of contents Does LexicMap support short reads? Does LexicMap support fungi genomes? How&rsquo;s the hardware requirement? Can I extract the matched sequences? How can I extract the upstream and downstream flanking sequences of matched regions? Why isn&rsquo;t the pident 100% when aligning with a sequence from the reference genomes? Why is LexicMap slow for batch searching? Does LexicMap support short reads? LexicMap is mainly designed for sequence alignment with a small number of queries (gene/plasmid/virus/phage sequences) longer than 200 bp by default." />
<meta name="description" content=" Table of contents Table of contents Does LexicMap support short reads? Does LexicMap support fungi genomes? How&rsquo;s the hardware requirement? Can I extract the matched sequences? How can I extract the upstream and downstream flanking sequences of matched regions? Why isn&rsquo;t the pident 100% when aligning with a sequence from the reference genomes? Why is LexicMap slow for batch searching? Does LexicMap support short reads? LexicMap is mainly designed for sequence alignment with a small number of queries (gene/plasmid/virus/phage sequences) longer than 200 bp by default. However, short queries can also be aligned." />

<title>FAQs | LexicMap: efficient sequence alignment against millions of prokaryotic genomes​</title>

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<meta property="og:description" content="Table of contents Table of contents Does LexicMap support short reads? Does LexicMap support fungi genomes? How’s the hardware requirement? Can I extract the matched sequences? How can I extract the upstream and downstream flanking sequences of matched regions? Why isn’t the pident 100% when aligning with a sequence from the reference genomes? Why is LexicMap slow for batch searching? Does LexicMap support short reads? LexicMap is mainly designed for sequence alignment with a small number of queries (gene/plasmid/virus/phage sequences) longer than 200 bp by default." />
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70 changes: 35 additions & 35 deletions index.html
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<p>Using LexicMap to search in the whole <strong>2,340,672</strong> Genbank+Refseq prokaryotic genomes with 48 CPUs.</p>
<div class="table-wrap"> <table>
<thead>
<tr>
<th style="text-align:left">Query</th>
<th style="text-align:right">Genome hits</th>
<th style="text-align:right">Time</th>
<th style="text-align:right">RAM</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left">A 1.3-kb gene</td>
<td style="text-align:right">37,164</td>
<td style="text-align:right">36s</td>
<td style="text-align:right">4.1GB</td>
</tr>
<tr>
<td style="text-align:left">A 1.5-kb 16S rRNA</td>
<td style="text-align:right">1,949,496</td>
<td style="text-align:right">10m41s</td>
<td style="text-align:right">14.1GB</td>
</tr>
<tr>
<td style="text-align:left">A 52.8-kb plasmid</td>
<td style="text-align:right">544,619</td>
<td style="text-align:right">19m20s</td>
<td style="text-align:right">19.3GB</td>
</tr>
<tr>
<td style="text-align:left">1003 AMR genes</td>
<td style="text-align:right">25,702,419</td>
<td style="text-align:right">187m40s</td>
<td style="text-align:right">55.4GB</td>
</tr>
</tbody>
<thead>
<tr>
<th style="text-align: left">Query</th>
<th style="text-align: right">Genome hits</th>
<th style="text-align: right">Time</th>
<th style="text-align: right">RAM</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align: left">A 1.3-kb gene</td>
<td style="text-align: right">37,164</td>
<td style="text-align: right">36s</td>
<td style="text-align: right">4.1GB</td>
</tr>
<tr>
<td style="text-align: left">A 1.5-kb 16S rRNA</td>
<td style="text-align: right">1,949,496</td>
<td style="text-align: right">10m41s</td>
<td style="text-align: right">14.1GB</td>
</tr>
<tr>
<td style="text-align: left">A 52.8-kb plasmid</td>
<td style="text-align: right">544,619</td>
<td style="text-align: right">19m20s</td>
<td style="text-align: right">19.3GB</td>
</tr>
<tr>
<td style="text-align: left">1003 AMR genes</td>
<td style="text-align: right">25,702,419</td>
<td style="text-align: right">187m40s</td>
<td style="text-align: right">55.4GB</td>
</tr>
</tbody>
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<p><em><strong>Blastn</strong> is unable to run with the same dataset on common servers as it requires &gt;2000 GB RAM</em>.</p>
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