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new command: utils index-density
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shenwei356 committed May 12, 2023
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98 changes: 98 additions & 0 deletions docs/faq/index.html
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How to tune parts of options when using preset profiling modes?
</a>

</li>

<li class="md-nav__item">
<a href="#are-the-elements-in-the-bloom-filters-uniformly-distributed" class="md-nav__link">
Are the elements in the bloom filters uniformly distributed?
</a>

</li>

</ul>
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How to tune parts of options when using preset profiling modes?
</a>

</li>

<li class="md-nav__item">
<a href="#are-the-elements-in-the-bloom-filters-uniformly-distributed" class="md-nav__link">
Are the elements in the bloom filters uniformly distributed?
</a>

</li>

</ul>
Expand Down Expand Up @@ -874,6 +888,90 @@ <h3 id="how-to-tune-parts-of-options-when-using-preset-profiling-modes">How to t
<p><s>Sorry it's not supported due to the limitation of the command-line argument parsers.
You need explicitly set all relevant options of the mode.</s></p>
<p>It's available since v0.8.2.</p>
<h3 id="are-the-elements-in-the-bloom-filters-uniformly-distributed">Are the elements in the bloom filters uniformly distributed?</h3>
<p>Some one asked me this when I were giving a talk of KMCP.
The answers is yes. I created a new command <a href="https://bioinf.shenwei.me/kmcp/usage/#index-density"><code>kmcp utils index-density</code></a> to plot the density of a index file.</p>
<p>Here's are some example outputs. The width is the number of bins and the height is the number of names (references or reference chunks).</p>
<ol>
<li>
<p>v2023.05-genbank-viral-_block001.uniki (FPR of bloom filter: 0.3), only a part of image is shown.</p>
<table>
<thead>
<tr>
<th align="left">file</th>
<th align="left">k</th>
<th align="left">canonical</th>
<th align="left">num-hashes</th>
<th align="left">num-sigs</th>
<th align="left">num-names</th>
</tr>
</thead>
<tbody>
<tr>
<td align="left">_block001.uniki</td>
<td align="left">21</td>
<td align="left">true</td>
<td align="left">1</td>
<td align="left">6395</td>
<td align="left">10400</td>
</tr>
</tbody>
</table>
<p><img alt="" src="../v2023.05-genbank-viral-_block001.uniki.part.jpg" /></p>
</li>
<li>
<p>v2023.05-refseq-fungi-_block001.uniki (FPR of bloom filter: 0.3)</p>
<table>
<thead>
<tr>
<th align="left">file</th>
<th align="left">k</th>
<th align="left">canonical</th>
<th align="left">num-hashes</th>
<th align="left">num-sigs</th>
<th align="left">num-names</th>
</tr>
</thead>
<tbody>
<tr>
<td align="left">_block001.uniki</td>
<td align="left">21</td>
<td align="left">true</td>
<td align="left">1</td>
<td align="left">2089979</td>
<td align="left">160</td>
</tr>
</tbody>
</table>
<p><img alt="" src="../v2023.05-refseq-fungi-_block001.uniki.jpg" /></p>
</li>
<li>
<p>v2023.05-refseq-fungi-_block002.uniki (FPR of bloom filter: 0.3)</p>
<table>
<thead>
<tr>
<th align="left">file</th>
<th align="left">k</th>
<th align="left">canonical</th>
<th align="left">num-hashes</th>
<th align="left">num-sigs</th>
<th align="left">num-names</th>
</tr>
</thead>
<tbody>
<tr>
<td align="left">_block002.uniki</td>
<td align="left">21</td>
<td align="left">true</td>
<td align="left">1</td>
<td align="left">2599648</td>
<td align="left">160</td>
</tr>
</tbody>
</table>
<p><img alt="" src="../v2023.05-refseq-fungi-_block002.uniki.jpg" /></p>
</li>
</ol>


</article>
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10 changes: 7 additions & 3 deletions docs/index.html
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</tr>
<tr>
<td align="left"><a href="https://bioinf.shenwei.me/kmcp/usage/#unik-info">utils unik-info</a></td>
<td align="left">Print information of .unik file</td>
<td align="left">Print information of .unik files</td>
</tr>
<tr>
<td align="left"><a href="https://bioinf.shenwei.me/kmcp/usage/#index-info">utils index-info</a></td>
<td align="left">Print information of index file</td>
<td align="left">Print information of index files</td>
</tr>
<tr>
<td align="left"><a href="https://bioinf.shenwei.me/kmcp/usage/#index-density">utils index-density</a></td>
<td align="left">Plot the density of a index file</td>
</tr>
<tr>
<td align="left"><a href="https://bioinf.shenwei.me/kmcp/usage/#ref-info">utils ref-info</a></td>
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kmcp profile search.kmcp.tsv.gz \
--taxid-map taxid.map \
--taxdump taxdump/ \
--out-prefix search.tsv.gz.k.profile \
--out-file search.tsv.gz.k.profile \
--metaphlan-report search.tsv.gz.m.profile \
--cami-report search.tsv.gz.c.profile \
--binning-result search.tsv.gz.binning.gz
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2 changes: 1 addition & 1 deletion docs/search/search_index.json
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26 changes: 13 additions & 13 deletions docs/sitemap.xml
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4 changes: 2 additions & 2 deletions docs/tutorial/profiling/index.html
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Expand Up @@ -1361,7 +1361,7 @@ <h4 id="commands_1"><strong>Commands</strong></h4>
--min-hic-ureads-qcov 0.75 \
--min-hic-ureads-prop 0.1 \
$sfile \
--out-prefix $sfile.kmcp.profile \
--out-file $sfile.kmcp.profile \
--metaphlan-report $sfile.metaphlan.profile \
--cami-report $sfile.cami.profile \
--sample-id "0" \
Expand All @@ -1370,7 +1370,7 @@ <h4 id="commands_1"><strong>Commands</strong></h4>
<h4 id="profiling-result-formats">Profiling result formats</h4>
<p>Taxonomic profiling output formats:</p>
<ul>
<li>KMCP (<code>-o/--out-prefix</code>).
<li>KMCP (<code>-o/--out-file</code>).
<strong>Note that: abundances are only computed for target references rather than
each taxon at all taxonomic ranks, so please output CAMI or MetaPhlAn format</strong>.</li>
<li>CAMI (<code>-M/--metaphlan-report</code>, <code>--metaphlan-report-version</code>, sample name: <code>-s/--sample-id</code>, taxonomy data: <code>--taxonomy-id</code>)</li>
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