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.
1237 lines
22 KiB
HTML
1237 lines
22 KiB
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Kmers and super-kmers
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Kmers and super-kmers
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Kmers and super-kmers
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Kmers
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</a>
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Super-kmers
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Canonical super-kmers
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</span>
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DNA encoding
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<span class="md-ellipsis">
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Low-complexity kmer filter
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</a>
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Minimizer selection
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Partitioning and indexing architecture
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Usage
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
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Usage
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superkmer
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index
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merge
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filter
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select
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query
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dump
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annotate
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<h1 id="kmers-and-super-kmers">Kmers and super-kmers</h1>
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<h2 id="kmers">Kmers</h2>
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<p>A <strong>kmer</strong> is a DNA subsequence of fixed length <span class="arithmatex">\(k\)</span>. Two constraints apply to <span class="arithmatex">\(k\)</span>, both enforced when a command starts (an invalid value exits immediately with an error):</p>
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<ul>
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<li><span class="arithmatex">\(k \in [11, 31]\)</span>: long enough to be specific, short enough to fit in a single 64-bit word at 2 bits/base (<span class="arithmatex">\(k \le 32\)</span> is the hard limit; <span class="arithmatex">\(k < 11\)</span> gives insufficient specificity).</li>
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<li><span class="arithmatex">\(k\)</span> <strong>is odd</strong>: an odd-length sequence can never equal its own reverse complement, so the two orientations of any kmer are always distinct. This is required for the canonical form (see <a href="../encoding/">DNA encoding</a>) to be well defined.</li>
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</ul>
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<h2 id="super-kmers">Super-kmers</h2>
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<p>A <strong>super-kmer</strong> is a maximal run of consecutive, overlapping kmers from a read that share the same canonical minimizer (see <a href="../minimizer_selection/">Minimizer selection</a>). Each kmer in the run overlaps the next by <span class="arithmatex">\(k-1\)</span> nucleotides. A super-kmer is capped at 256 nucleotides; a longer run is split at that boundary.</p>
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<p>For a random minimizer of length <span class="arithmatex">\(m\)</span> over kmers of length <span class="arithmatex">\(k\)</span>, the expected length of a super-kmer is approximately (Golan & Shur 2025; Zheng <em>et al.</em> 2020)<sup id="fnref:Zheng2020-ji"><a class="footnote-ref" href="#fn:Zheng2020-ji">1</a></sup> <sup id="fnref:Golan2025-xf"><a class="footnote-ref" href="#fn:Golan2025-xf">2</a></sup>:</p>
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<div class="arithmatex">\[L_{\text{nt}} \approx \frac{k-m+2}{2} + k - 1\]</div>
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<p>For <span class="arithmatex">\(k=31\)</span>, <span class="arithmatex">\(m=13\)</span> this is about 40 nucleotides; in practice super-kmers rarely exceed a few dozen nucleotides.</p>
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<h3 id="canonical-super-kmers">Canonical super-kmers</h3>
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<p>A <strong>canonical super-kmer</strong> is the lexicographic minimum of a super-kmer and its reverse complement. When a read and its reverse complement are both encountered, they produce super-kmers that are reverse complements of each other; both reduce to the same canonical super-kmer, so a genomic region is represented once regardless of which strand was read.</p>
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<p>Super-kmers are the unit of work used throughout construction and querying: sequences are decomposed into super-kmers first, and every downstream step (partition routing, deduplication, counting) operates on them rather than on individual kmers.</p>
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<hr />
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<ol>
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<li id="fn:Zheng2020-ji">
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<p>Zheng, H., Kingsford, C. & Marçais, G. (2020). <a href="https://doi.org/10.1093/bioinformatics/btaa472">Improved design and analysis of practical minimizers</a>. <em>Bioinformatics (Oxford, England)</em>, 36, i119--i127. <a class="footnote-backref" href="#fnref:Zheng2020-ji" title="Jump back to footnote 1 in the text">↩</a></p>
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<li id="fn:Golan2025-xf">
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<p>Golan, S. & Shur, A.M. (2025). <a href="https://doi.org/10.1007/978-3-031-82670-2\_25">Expected density of random minimizers</a>. In: <em>Lecture notes in computer science</em>, Lecture notes in computer science. Springer Nature Switzerland, Cham, pp. 347--360. <a class="footnote-backref" href="#fnref:Golan2025-xf" title="Jump back to footnote 2 in the text">↩</a></p>
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