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<h1 id="index">index</h1>
<p>Build a genome index from one or more sequence files. Construction proceeds in phases (scatter → dereplicate → count → layered MPHF), described in <a href="../../formats/index_layout/">On-disk storage</a>.</p>
<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>index<span class="w"> </span>-o<span class="w"> </span>OUTPUT<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>
</code></pre></div>
<h2 id="arguments">Arguments</h2>
<table>
<thead>
<tr>
<th>Argument</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td><code>INPUTS...</code></td>
<td>Input sequence files or directories (FASTA/FASTQ/GenBank, gzip optional). If omitted, reads from stdin.</td>
</tr>
</tbody>
</table>
<h2 id="options">Options</h2>
<table>
<thead>
<tr>
<th>Option</th>
<th>Default</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td><code>-o, --output</code></td>
<td>— (required)</td>
<td>Output index directory</td>
</tr>
<tr>
<td><code>--force</code></td>
<td>off</td>
<td>Overwrite an existing output directory</td>
</tr>
<tr>
<td><code>--label</code></td>
<td>input file name without extension</td>
<td>Genome label stored in the index</td>
</tr>
<tr>
<td><code>--meta KEY=VALUE</code></td>
<td>none</td>
<td>Attach a categorical metadata field to the genome (repeatable)</td>
</tr>
<tr>
<td><code>-k, --kmer-size</code></td>
<td><code>31</code></td>
<td>Kmer size (odd, in [11, 31])</td>
</tr>
<tr>
<td><code>-m, --minimizer-size</code></td>
<td><code>11</code></td>
<td>Minimizer size (odd, in <span class="arithmatex">\([3, k-1]\)</span>)</td>
</tr>
<tr>
<td><code>--theta</code></td>
<td><code>0.7</code></td>
<td>Entropy threshold for the low-complexity filter</td>
</tr>
<tr>
<td><code>--level-max</code></td>
<td><code>6</code></td>
<td>Maximum sub-word size for the entropy score</td>
</tr>
<tr>
<td><code>-p, --partitions</code></td>
<td><code>256</code></td>
<td>Number of partitions (rounded up to a power of 2)</td>
</tr>
<tr>
<td><code>-T, --threads</code></td>
<td>detected core count</td>
<td>Number of worker threads</td>
</tr>
<tr>
<td><code>--max-open-files</code></td>
<td><code>threads / 4</code> (min 1)</td>
<td>Maximum number of input files open simultaneously</td>
</tr>
<tr>
<td><code>--min-abundance</code></td>
<td><code>1</code></td>
<td>Minimum abundance (inclusive) for a kmer to be retained</td>
</tr>
<tr>
<td><code>--max-abundance</code></td>
<td>none</td>
<td>Maximum abundance (inclusive)</td>
</tr>
<tr>
<td><code>--with-counts</code></td>
<td>off</td>
<td>Store per-kmer counts; otherwise only presence/absence is stored</td>
</tr>
<tr>
<td><code>--keep-intermediate</code></td>
<td>off</td>
<td>Keep intermediate build files instead of deleting them after construction</td>
</tr>
<tr>
<td><code>--approx</code></td>
<td>off</td>
<td>Use approximate evidence (Findere fingerprint) instead of exact evidence</td>
</tr>
<tr>
<td><code>-z, --findere-z</code></td>
<td>see below</td>
<td>Findere z parameter: number of consecutive kmers that must all match (approximate evidence only)</td>
</tr>
<tr>
<td><code>--evidence-bits</code></td>
<td>see below</td>
<td>Fingerprint bits per slot (b), approximate evidence only</td>
</tr>
<tr>
<td><code>--fp</code></td>
<td>see below</td>
<td>Target false-positive rate per z-window, approximate evidence only</td>
</tr>
<tr>
<td><code>--block-size</code></td>
<td><code>1</code></td>
<td>Block size, in unitigs, for the exact on-disk index (rounded up to a power of 2)</td>
</tr>
</tbody>
</table>
<h2 id="exact-vs-approximate-evidence">Exact vs. approximate evidence</h2>
<p>By default, an index stores <strong>exact</strong> evidence: a kmer is either present or absent (or has an exact count with <code>--with-counts</code>), with no false positives.</p>
<p>With <code>--approx</code>, evidence is stored as a compact <strong>fingerprint</strong> instead, trading a small, tunable false-positive rate for reduced memory/disk usage. The false-positive model is:</p>
<div class="arithmatex">\[FP = \frac{1}{2^{b \cdot z}}\]</div>
<p>where <span class="arithmatex">\(b\)</span> is <code>--evidence-bits</code> and <span class="arithmatex">\(z\)</span> is <code>--findere-z</code>. Any two of <code>-z</code>, <code>--evidence-bits</code>, <code>--fp</code> can be given and the third is derived; if none are given, defaults are <span class="arithmatex">\(b=8\)</span>, <span class="arithmatex">\(z=1\)</span> (<span class="arithmatex">\(FP \approx 1/256\)</span>). See <a href="../estimate/"><code>estimate</code></a> to explore this trade-off before building an index, and <a href="../reindex/"><code>reindex</code></a> to convert an existing index between the two representations.</p>
<p><code>z</code> must be strictly less than k: the effective indexed kmer length under approximate evidence is k−z+1.</p>


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