1296 lines
24 KiB
HTML
1296 lines
24 KiB
HTML
|
||
<!doctype html>
|
||
<html lang="en" class="no-js">
|
||
<head>
|
||
|
||
<meta charset="utf-8">
|
||
<meta name="viewport" content="width=device-width,initial-scale=1">
|
||
|
||
|
||
|
||
|
||
<link rel="prev" href="../minimizer_selection/">
|
||
|
||
|
||
<link rel="next" href="../../usage/superkmer/">
|
||
|
||
|
||
|
||
|
||
|
||
<link rel="icon" href="../../assets/images/favicon.png">
|
||
<meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.7.6">
|
||
|
||
|
||
|
||
<title>Partitioning and indexing architecture - obikmer — User Guide</title>
|
||
|
||
|
||
|
||
<link rel="stylesheet" href="../../assets/stylesheets/main.484c7ddc.min.css">
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
|
||
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:300,300i,400,400i,700,700i%7CRoboto+Mono:400,400i,700,700i&display=fallback">
|
||
<style>:root{--md-text-font:"Roboto";--md-code-font:"Roboto Mono"}</style>
|
||
|
||
|
||
|
||
<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>
|
||
|
||
|
||
|
||
|
||
|
||
</head>
|
||
|
||
|
||
<body dir="ltr">
|
||
|
||
|
||
<input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="__drawer" autocomplete="off">
|
||
<input class="md-toggle" data-md-toggle="search" type="checkbox" id="__search" autocomplete="off">
|
||
<label class="md-overlay" for="__drawer"></label>
|
||
<div data-md-component="skip">
|
||
|
||
|
||
<a href="#partitioning-and-indexing-architecture" class="md-skip">
|
||
Skip to content
|
||
</a>
|
||
|
||
</div>
|
||
<div data-md-component="announce">
|
||
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<header class="md-header md-header--shadow" data-md-component="header">
|
||
<nav class="md-header__inner md-grid" aria-label="Header">
|
||
<a href="../.." title="obikmer — User Guide" class="md-header__button md-logo" aria-label="obikmer — User Guide" data-md-component="logo">
|
||
|
||
|
||
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
|
||
|
||
</a>
|
||
<label class="md-header__button md-icon" for="__drawer">
|
||
|
||
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M3 6h18v2H3zm0 5h18v2H3zm0 5h18v2H3z"/></svg>
|
||
</label>
|
||
<div class="md-header__title" data-md-component="header-title">
|
||
<div class="md-header__ellipsis">
|
||
<div class="md-header__topic">
|
||
<span class="md-ellipsis">
|
||
obikmer — User Guide
|
||
</span>
|
||
</div>
|
||
<div class="md-header__topic" data-md-component="header-topic">
|
||
<span class="md-ellipsis">
|
||
|
||
Partitioning and indexing architecture
|
||
|
||
</span>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
<script>var palette=__md_get("__palette");if(palette&&palette.color){if("(prefers-color-scheme)"===palette.color.media){var media=matchMedia("(prefers-color-scheme: light)"),input=document.querySelector(media.matches?"[data-md-color-media='(prefers-color-scheme: light)']":"[data-md-color-media='(prefers-color-scheme: dark)']");palette.color.media=input.getAttribute("data-md-color-media"),palette.color.scheme=input.getAttribute("data-md-color-scheme"),palette.color.primary=input.getAttribute("data-md-color-primary"),palette.color.accent=input.getAttribute("data-md-color-accent")}for(var[key,value]of Object.entries(palette.color))document.body.setAttribute("data-md-color-"+key,value)}</script>
|
||
|
||
|
||
|
||
|
||
</nav>
|
||
|
||
</header>
|
||
|
||
<div class="md-container" data-md-component="container">
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<main class="md-main" data-md-component="main">
|
||
<div class="md-main__inner md-grid">
|
||
|
||
|
||
|
||
<div class="md-sidebar md-sidebar--primary" data-md-component="sidebar" data-md-type="navigation" >
|
||
<div class="md-sidebar__scrollwrap">
|
||
<div class="md-sidebar__inner">
|
||
|
||
|
||
|
||
|
||
<nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
|
||
<label class="md-nav__title" for="__drawer">
|
||
<a href="../.." title="obikmer — User Guide" class="md-nav__button md-logo" aria-label="obikmer — User Guide" data-md-component="logo">
|
||
|
||
|
||
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
|
||
|
||
</a>
|
||
obikmer — User Guide
|
||
</label>
|
||
|
||
<ul class="md-nav__list" data-md-scrollfix>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../.." class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Home
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../installation/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Installation
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item md-nav__item--active md-nav__item--nested">
|
||
|
||
|
||
|
||
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
|
||
|
||
|
||
<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Theory
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
<span class="md-nav__icon md-icon"></span>
|
||
</label>
|
||
|
||
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
|
||
<label class="md-nav__title" for="__nav_3">
|
||
<span class="md-nav__icon md-icon"></span>
|
||
|
||
|
||
Theory
|
||
|
||
|
||
</label>
|
||
<ul class="md-nav__list" data-md-scrollfix>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../kmers_and_superkmers/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Kmers and super-kmers
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../encoding/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
DNA encoding
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../entropy_filter/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Low-complexity kmer filter
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../minimizer_selection/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Minimizer selection
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item md-nav__item--active">
|
||
|
||
<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
|
||
|
||
|
||
|
||
|
||
|
||
<label class="md-nav__link md-nav__link--active" for="__toc">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Partitioning and indexing architecture
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
<span class="md-nav__icon md-icon"></span>
|
||
</label>
|
||
|
||
<a href="./" class="md-nav__link md-nav__link--active">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Partitioning and indexing architecture
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
|
||
|
||
|
||
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<label class="md-nav__title" for="__toc">
|
||
<span class="md-nav__icon md-icon"></span>
|
||
Table of contents
|
||
</label>
|
||
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
|
||
|
||
<li class="md-nav__item">
|
||
<a href="#routing" class="md-nav__link">
|
||
<span class="md-ellipsis">
|
||
|
||
Routing
|
||
|
||
</span>
|
||
</a>
|
||
|
||
</li>
|
||
|
||
<li class="md-nav__item">
|
||
<a href="#why-hashing-is-necessary" class="md-nav__link">
|
||
<span class="md-ellipsis">
|
||
|
||
Why hashing is necessary
|
||
|
||
</span>
|
||
</a>
|
||
|
||
</li>
|
||
|
||
<li class="md-nav__item">
|
||
<a href="#parameter-guidance" class="md-nav__link">
|
||
<span class="md-ellipsis">
|
||
|
||
Parameter guidance
|
||
|
||
</span>
|
||
</a>
|
||
|
||
</li>
|
||
|
||
</ul>
|
||
|
||
</nav>
|
||
|
||
</li>
|
||
|
||
|
||
|
||
|
||
</ul>
|
||
</nav>
|
||
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item md-nav__item--nested">
|
||
|
||
|
||
|
||
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
|
||
|
||
|
||
<label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Usage
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
<span class="md-nav__icon md-icon"></span>
|
||
</label>
|
||
|
||
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
|
||
<label class="md-nav__title" for="__nav_4">
|
||
<span class="md-nav__icon md-icon"></span>
|
||
|
||
|
||
Usage
|
||
|
||
|
||
</label>
|
||
<ul class="md-nav__list" data-md-scrollfix>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/superkmer/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
superkmer
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/index_command/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
index
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/merge/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
merge
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/filter/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
filter
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/select/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
select
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/query/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
query
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/dump/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
dump
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/annotate/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
annotate
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/phylo/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
phylo
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/name-tree/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
name-tree
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/unitig/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
unitig
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/estimate/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
estimate
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/reindex/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
reindex
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/utils/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
utils
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/pack/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
pack
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../usage/predicates/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Predicates and taxonomy paths
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
</ul>
|
||
</nav>
|
||
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item md-nav__item--nested">
|
||
|
||
|
||
|
||
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
|
||
|
||
|
||
<label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Formats
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
<span class="md-nav__icon md-icon"></span>
|
||
</label>
|
||
|
||
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
|
||
<label class="md-nav__title" for="__nav_5">
|
||
<span class="md-nav__icon md-icon"></span>
|
||
|
||
|
||
Formats
|
||
|
||
|
||
</label>
|
||
<ul class="md-nav__list" data-md-scrollfix>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../formats/index_layout/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Index construction and on-disk layout
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
|
||
</ul>
|
||
</nav>
|
||
|
||
</li>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<li class="md-nav__item">
|
||
<a href="../../architecture/" class="md-nav__link">
|
||
|
||
|
||
|
||
<span class="md-ellipsis">
|
||
|
||
|
||
Architecture notes
|
||
|
||
|
||
|
||
</span>
|
||
|
||
|
||
|
||
</a>
|
||
</li>
|
||
|
||
|
||
|
||
</ul>
|
||
</nav>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
<div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
|
||
<div class="md-sidebar__scrollwrap">
|
||
<div class="md-sidebar__inner">
|
||
|
||
|
||
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<label class="md-nav__title" for="__toc">
|
||
<span class="md-nav__icon md-icon"></span>
|
||
Table of contents
|
||
</label>
|
||
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
|
||
|
||
<li class="md-nav__item">
|
||
<a href="#routing" class="md-nav__link">
|
||
<span class="md-ellipsis">
|
||
|
||
Routing
|
||
|
||
</span>
|
||
</a>
|
||
|
||
</li>
|
||
|
||
<li class="md-nav__item">
|
||
<a href="#why-hashing-is-necessary" class="md-nav__link">
|
||
<span class="md-ellipsis">
|
||
|
||
Why hashing is necessary
|
||
|
||
</span>
|
||
</a>
|
||
|
||
</li>
|
||
|
||
<li class="md-nav__item">
|
||
<a href="#parameter-guidance" class="md-nav__link">
|
||
<span class="md-ellipsis">
|
||
|
||
Parameter guidance
|
||
|
||
</span>
|
||
</a>
|
||
|
||
</li>
|
||
|
||
</ul>
|
||
|
||
</nav>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
<div class="md-content" data-md-component="content">
|
||
|
||
<article class="md-content__inner md-typeset">
|
||
|
||
|
||
|
||
|
||
|
||
<h1 id="partitioning-and-indexing-architecture">Partitioning and indexing architecture</h1>
|
||
<p>An index is split into a fixed number of <strong>partitions</strong>, each handling an independent, disjoint slice of the kmer space. Partitioning keeps the working set of each stage small enough to process efficiently and enables parallel construction and querying.</p>
|
||
<h2 id="routing">Routing</h2>
|
||
<p>The canonical minimizer of a super-kmer (see <a href="../minimizer_selection/">Minimizer selection</a>) is hashed to produce a <span class="arithmatex">\(p\)</span>-bit routing value that selects the destination partition:</p>
|
||
<div class="highlight"><pre><span></span><code>canonical minimizer → hash(minimizer) → p-bit value → partition index
|
||
</code></pre></div>
|
||
<p>The routing value is recomputed whenever it is needed (during construction and again at query time) rather than stored — it is not part of the on-disk super-kmer representation.</p>
|
||
<p>Within a partition, kmers are indexed as plain values via a minimal perfect hash function (see <a href="../../formats/index_layout/">On-disk storage</a>); the minimizer plays no further role once a super-kmer has reached its partition.</p>
|
||
<h2 id="why-hashing-is-necessary">Why hashing is necessary</h2>
|
||
<p>A canonical minimizer is an m-mer (<span class="arithmatex">\(m \in \{9, 11, 13, 15\}\)</span>), and its distribution over all possible m-mer values is not uniform — as the lexicographic minimum of a window, small values are systematically over-represented (Golan & Shur 2025; Kille <em>et al.</em> 2023; Pan & Reinert 2024; Zheng <em>et al.</em> 2020, 2021)<sup id="fnref:Zheng2020-ji"><a class="footnote-ref" href="#fn:Zheng2020-ji">1</a></sup> <sup id="fnref:Zheng2021-cc"><a class="footnote-ref" href="#fn:Zheng2021-cc">2</a></sup> <sup id="fnref:Pan2024-hb"><a class="footnote-ref" href="#fn:Pan2024-hb">3</a></sup> <sup id="fnref:Kille2023-px"><a class="footnote-ref" href="#fn:Kille2023-px">4</a></sup> <sup id="fnref:Golan2025-xf"><a class="footnote-ref" href="#fn:Golan2025-xf">5</a></sup>. Routing directly on the raw minimizer value would therefore produce badly unbalanced partitions.</p>
|
||
<p>Hashing the minimizer before routing redistributes this skewed distribution uniformly across partitions. This works reliably because the number of partition-index bits <span class="arithmatex">\(p\)</span> is chosen well below the number of bits available in the minimizer (<span class="arithmatex">\(2m\)</span>): even with strong bias in the minimizer distribution, the hash has enough entropy margin to absorb it, provided the number of distinct minimizers actually observed is much larger than the number of partitions.</p>
|
||
<h2 id="parameter-guidance">Parameter guidance</h2>
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Minimizer size <span class="arithmatex">\(m\)</span></th>
|
||
<th>Minimizer bits (<span class="arithmatex">\(2m\)</span>)</th>
|
||
<th>Typical partition-index bits <span class="arithmatex">\(p\)</span></th>
|
||
<th>Partitions</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td>9</td>
|
||
<td>18</td>
|
||
<td>6–8</td>
|
||
<td>64–256</td>
|
||
</tr>
|
||
<tr>
|
||
<td>11</td>
|
||
<td>22</td>
|
||
<td>8–10</td>
|
||
<td>256–1 024</td>
|
||
</tr>
|
||
<tr>
|
||
<td>13</td>
|
||
<td>26</td>
|
||
<td>10–12</td>
|
||
<td>1 024–4 096</td>
|
||
</tr>
|
||
<tr>
|
||
<td>15</td>
|
||
<td>30</td>
|
||
<td>10–14</td>
|
||
<td>1 024–16 384</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>The number of partitions must satisfy <span class="arithmatex">\(p \le 2m\)</span>, and in practice <span class="arithmatex">\(p\)</span> is chosen well below that bound to leave a comfortable entropy margin. For <span class="arithmatex">\(k=31\)</span>, <span class="arithmatex">\(m=13\)</span>, <span class="arithmatex">\(p=10\)</span> (1024 partitions), partition load is well balanced on real genomic data.</p>
|
||
<div class="footnote">
|
||
<hr />
|
||
<ol>
|
||
<li id="fn:Zheng2020-ji">
|
||
<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>
|
||
</li>
|
||
<li id="fn:Zheng2021-cc">
|
||
<p>Zheng, H., Kingsford, C. & Marçais, G. (2021). <a href="https://doi.org/10.1093/bioinformatics/btab313">Sequence-specific minimizers via polar sets</a>. <em>Bioinformatics (Oxford, England)</em>, 37, i187--i195. <a class="footnote-backref" href="#fnref:Zheng2021-cc" title="Jump back to footnote 2 in the text">↩</a></p>
|
||
</li>
|
||
<li id="fn:Pan2024-hb">
|
||
<p>Pan, C. & Reinert, K. (2024). <a href="https://doi.org/10.1093/bioinformatics/btae045">A simple refined DNA minimizer operator enables 2-fold faster computation</a>. <em>Bioinformatics (Oxford, England)</em>, 40. <a class="footnote-backref" href="#fnref:Pan2024-hb" title="Jump back to footnote 3 in the text">↩</a></p>
|
||
</li>
|
||
<li id="fn:Kille2023-px">
|
||
<p>Kille, B., Garrison, E., Treangen, T.J. & Phillippy, A.M. (2023). <a href="https://doi.org/10.1093/bioinformatics/btad512">Minmers are a generalization of minimizers that enable unbiased local jaccard estimation</a>. <em>Bioinformatics (Oxford, England)</em>, 39. <a class="footnote-backref" href="#fnref:Kille2023-px" title="Jump back to footnote 4 in the text">↩</a></p>
|
||
</li>
|
||
<li id="fn:Golan2025-xf">
|
||
<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 5 in the text">↩</a></p>
|
||
</li>
|
||
</ol>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
</article>
|
||
</div>
|
||
|
||
|
||
<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
|
||
</div>
|
||
|
||
</main>
|
||
|
||
<footer class="md-footer">
|
||
|
||
<div class="md-footer-meta md-typeset">
|
||
<div class="md-footer-meta__inner md-grid">
|
||
<div class="md-copyright">
|
||
|
||
|
||
Made with
|
||
<a href="https://squidfunk.github.io/mkdocs-material/" target="_blank" rel="noopener">
|
||
Material for MkDocs
|
||
</a>
|
||
|
||
</div>
|
||
|
||
</div>
|
||
</div>
|
||
</footer>
|
||
|
||
</div>
|
||
<div class="md-dialog" data-md-component="dialog">
|
||
<div class="md-dialog__inner md-typeset"></div>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
<script id="__config" type="application/json">{"annotate": null, "base": "../..", "features": [], "search": "../../assets/javascripts/workers/search.2c215733.min.js", "tags": null, "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": null}</script>
|
||
|
||
|
||
<script src="../../assets/javascripts/bundle.79ae519e.min.js"></script>
|
||
|
||
<script src="https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js"></script>
|
||
|
||
|
||
</body>
|
||
</html> |