1364 lines
23 KiB
HTML
1364 lines
23 KiB
HTML
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<!doctype html>
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<meta name="viewport" content="width=device-width,initial-scale=1">
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<link rel="prev" href="../superkmer/">
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<link rel="next" href="../merge/">
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<meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.7.6">
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<style>:root{--md-text-font:"Roboto";--md-code-font:"Roboto Mono"}</style>
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<script>__md_scope=new URL("../..",location),__md_hash=e=>[...e].reduce(((e,_)=>(e<<5)-e+_.charCodeAt(0)),0),__md_get=(e,_=localStorage,t=__md_scope)=>JSON.parse(_.getItem(t.pathname+"."+e)),__md_set=(e,_,t=localStorage,a=__md_scope)=>{try{t.setItem(a.pathname+"."+e,JSON.stringify(_))}catch(e){}}</script>
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<body dir="ltr">
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<input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="__drawer" autocomplete="off">
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<div data-md-component="skip">
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<a href="#index" class="md-skip">
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Skip to content
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<div class="md-header__ellipsis">
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<div class="md-header__topic">
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<span class="md-ellipsis">
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obikmer — User Guide
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</span>
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</div>
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<div class="md-header__topic" data-md-component="header-topic">
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<span class="md-ellipsis">
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index
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</nav>
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<div class="md-container" data-md-component="container">
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<main class="md-main" data-md-component="main">
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<div class="md-main__inner md-grid">
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<nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
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</a>
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obikmer — User Guide
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../.." class="md-nav__link">
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<span class="md-ellipsis">
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Home
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../installation/" class="md-nav__link">
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<span class="md-ellipsis">
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Installation
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</span>
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</a>
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</li>
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<li class="md-nav__item md-nav__item--nested">
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<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
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<span class="md-ellipsis">
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Theory
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</span>
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
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<label class="md-nav__title" for="__nav_3">
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<span class="md-nav__icon md-icon"></span>
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Theory
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../../theory/kmers_and_superkmers/" class="md-nav__link">
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<span class="md-ellipsis">
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Kmers and super-kmers
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../theory/encoding/" class="md-nav__link">
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<span class="md-ellipsis">
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DNA encoding
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../theory/entropy_filter/" class="md-nav__link">
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<span class="md-ellipsis">
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Low-complexity kmer filter
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../theory/minimizer_selection/" class="md-nav__link">
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<span class="md-ellipsis">
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Minimizer selection
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../theory/indexing_architecture/" class="md-nav__link">
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<span class="md-ellipsis">
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Partitioning and indexing architecture
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</span>
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</a>
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</li>
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</ul>
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</nav>
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</li>
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<li class="md-nav__item md-nav__item--active md-nav__item--nested">
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
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<label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
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<span class="md-ellipsis">
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Usage
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</span>
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
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<label class="md-nav__title" for="__nav_4">
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<span class="md-nav__icon md-icon"></span>
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Usage
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../superkmer/" class="md-nav__link">
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<span class="md-ellipsis">
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superkmer
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||
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</span>
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</a>
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</li>
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<li class="md-nav__item md-nav__item--active">
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<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
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<label class="md-nav__link md-nav__link--active" for="__toc">
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<span class="md-ellipsis">
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index
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</span>
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<span class="md-nav__icon md-icon"></span>
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</label>
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<a href="./" class="md-nav__link md-nav__link--active">
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<span class="md-ellipsis">
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index
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</span>
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</a>
|
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<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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<label class="md-nav__title" for="__toc">
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<span class="md-nav__icon md-icon"></span>
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Table of contents
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</label>
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<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="#arguments" class="md-nav__link">
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<span class="md-ellipsis">
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Arguments
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="#options" class="md-nav__link">
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<span class="md-ellipsis">
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Options
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</span>
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||
</a>
|
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||
</li>
|
||
|
||
<li class="md-nav__item">
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||
<a href="#exact-vs-approximate-evidence" class="md-nav__link">
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||
<span class="md-ellipsis">
|
||
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||
Exact vs. approximate evidence
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||
|
||
</span>
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||
</a>
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||
|
||
</li>
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||
|
||
</ul>
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</nav>
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</li>
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||
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||
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||
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||
<li class="md-nav__item">
|
||
<a href="../merge/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
merge
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../filter/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
filter
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../select/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
select
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../query/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
query
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../dump/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
dump
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
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|
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|
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|
||
|
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|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../annotate/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
annotate
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
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|
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|
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|
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|
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|
||
|
||
|
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|
||
<li class="md-nav__item">
|
||
<a href="../phylo/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
phylo
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
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</a>
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estimate
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Predicates and taxonomy paths
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Formats
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Index construction and on-disk layout
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Architecture notes
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Arguments
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Options
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|
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|
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|
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<a href="#exact-vs-approximate-evidence" class="md-nav__link">
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|
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Exact vs. approximate evidence
|
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|
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|
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<article class="md-content__inner md-typeset">
|
||
|
||
|
||
|
||
|
||
|
||
<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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