Eric Coissac
caf59b5658
Renames the reindex command to convert across all usage guides and navigation menus. Adds documentation for the newly introduced name-tree command. Updates flag references, such as replacing --metric with --distance in pack and phylo modules, and adjusts MkDocs configuration to match the revised structure. All changes are strictly limited to documentation and configuration files.
1244 lines
20 KiB
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1244 lines
20 KiB
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DNA encoding
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Partitioning and indexing architecture
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index
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merge
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filter
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select
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dump
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annotate
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phylo
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<h1 id="superkmer">superkmer</h1>
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<p>Extract super-kmers from one or more sequence files and write them to stdout, without building a full index. Useful for inspecting or piping the super-kmer decomposition of a dataset.</p>
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<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>superkmer<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span><span class="w"> </span><span class="o">[</span>INPUTS...<span class="o">]</span>
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</code></pre></div>
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<h2 id="arguments">Arguments</h2>
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<table>
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<thead>
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<tr>
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<th>Argument</th>
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<th>Description</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td><code>INPUTS...</code></td>
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<td>Input sequence files or directories (FASTA/FASTQ/GenBank, gzip optional). If omitted, reads from stdin.</td>
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</tr>
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</tbody>
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</table>
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<h2 id="options">Options</h2>
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<table>
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<thead>
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<tr>
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<th>Option</th>
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<th>Default</th>
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<th>Description</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td><code>-k, --kmer-size</code></td>
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<td><code>31</code></td>
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<td>Kmer size (must be odd, in [11, 31])</td>
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</tr>
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<tr>
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<td><code>-m, --minimizer-size</code></td>
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<td><code>11</code></td>
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<td>Minimizer size (must be odd, in <span class="arithmatex">\([3, k-1]\)</span>)</td>
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</tr>
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<tr>
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<td><code>--theta</code></td>
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<td><code>0.7</code></td>
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<td>Entropy threshold; kmers with a normalized entropy at or below this value are excluded</td>
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</tr>
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<tr>
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<td><code>--level-max</code></td>
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<td><code>6</code></td>
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<td>Maximum sub-word size used for the entropy score</td>
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</tr>
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<tr>
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<td><code>-p, --partitions</code></td>
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<td><code>256</code></td>
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<td>Number of partitions (rounded up to the next power of 2)</td>
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</tr>
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<tr>
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<td><code>-T, --threads</code></td>
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<td>detected core count</td>
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<td>Number of worker threads</td>
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</tr>
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<tr>
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<td><code>--max-open-files</code></td>
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<td><code>threads / 4</code> (min 1)</td>
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<td>Maximum number of input files open simultaneously</td>
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</tr>
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</tbody>
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</table>
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<p>Output is written to stdout in the internal scatter format used by <code>index</code>; it is primarily intended to be piped into other tools or inspected for debugging.</p>
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