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cmd_cluster_smallmem.html
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cmd_cluster_smallmem.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
<html lang="en">
<head>
<meta content="en-us" http-equiv="Content-Language"/>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type"/>
<meta content="no-cache, no-store, must-revalidate" http-equiv="Cache-Control"/>
<meta content="no-cache" http-equiv="Pragma"/>
<meta content="0" http-equiv="Expires"/>
<title>
allpairs_global command
</title>
<link href="stylesx.css" rel="stylesheet" type="text/css"/>
<style type="text/css">
body.c4 {background-color:#c0c0c0;}
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a.SideButton:hover { color:orange; }
</style>
</head>
<body style="background-color:#c0c0c0;">
<div>
<a href="https://drive5.com/usearch">
<img alt="USEARCH v12" src="usearch12_banner.jpg" style="position:absolute; top:40px; left:10px; padding:0px; border:0px;"/>
</a>
</div>
<div style="position:absolute; top:115px; left:10px; width:850px; background-color:#ffffff; min-height:500px">
<div style="position:relative; float:left; background-color:#696969; width:125px; left: 0px; min-height:500px; padding:5px; height: 125px;">
<div class="SideButtonPara" style="text-align:center; padding-top:5px;">
<a class="SideButton" href="index.html">
Docs home
</a>
<br/>
<hr style="border:0; border-bottom: 1px solid white;"/>
<a class="SideButton" href="cmds.html">
Commands
</a>
<br/>
<a class="SideButton" href="topics.html">
Topics
</a>
<br/>
<a class="SideButton" href="citation.html">
Publications
</a>
<br/>
</div>
</div>
<div class="ManText" style="left:20px; position: absolute; left:135px; width:695px; background-color:white; padding:10px">
<h1>
cluster_smallmem command
</h1>
<span class="ManText">
<b>
See also
<br/>
</b>
<a href="cmd_cluster_fast.html">
cluster_fast
</a>
<br/>
<a href="cmd_cluster_otus.html">
cluster_otus
</a>
<br/>
<a href="DELETE_URL">
cluster_agg
</a>
<br/>
<a href="DELETE_URL">
cluster_aggd
</a>
</span>
<p>
<span class="ManText">
Clusters sequences in a
<a href="fasta_files.html">
FASTA
</a>
or
<a href="fastq_files.html">
FASTQ
</a>
file using a variant of the
<a href="uclust_algo.html">
UCLUST algorithm
</a>
designed to minimize memory use.
</span>
</p>
<p>
<span class="ManText">
It's is the user's responsibility to sort the input sequences in an appropriate order before running cluster_smallmem; see
<a href="uclust_sortorder.html">
UCLUST sort order
</a>
for discussion. By default, input sequences are expected to be sorted by decreasing length. If some other sort order is used, the -
<a href="opt_sortedby.html">
sortedby
</a>
option should be specified. Valid values are length (default),
<a href="size_annot.html">
size
</a>
and other. If -sortedby other is specified, then USEARCH does not assume or check for any particular order. See also
<a href="DELETE_URL">
sortbysize
</a>
and
<a href="DELETE_URL">
sortbylength
</a>
.
</span>
</p>
<p>
<span class="ManText">
An identity threshold must be specified using the -
<a href="opt_id.html">
id option
</a>
.
</span>
</p>
<p>
<span class="ManText">
Multithreading is not supported as this would require significant memory overhead.
</span>
</p>
<p>
<span class="ManText">
By default, nucleotide matching is done on the forward strand only. For matching on both strands, use -
<a href="opt_strand.html">
strand
</a>
both.
</span>
</p>
<p>
<b>
<span class="ManText">
See also
</span>
</b>
<span class="ManText">
<br/>
<a href="output_files.html">
Standard output file options
</a>
<br/>
</span>
<span class="ManText">
<a href="accept_options.html">
Accept options
</a>
<br/>
<a href="indexing_options.html">
Indexing options
</a>
<br/>
<a href="termination_options.html">
Termination options
</a>
<br/>
<a href="masking_options.html">
Masking options
</a>
<br/>
<a href="aln_params.html">
Alignment parameters
</a>
<br/>
<a href="aln_heuristics.html">
Alignment heuristics
</a>
</span>
<br/>
<span class="ManText">
<a href="cluster_sizes.html">
Cluster sizes
</a>
</span>
<br/>
<span class="ManText">
<a href="memory.html">
Memory requirements
</a>
</span>
</p>
<p>
<span class="ManText c3">
Example
</span>
</p>
<p>
<span class="ManCode">
usearch -cluster_smallmem query.fasta -id 0.9
-centroids nr.fasta -uc clusters.uc
<br/>
</span>
</p>
</div>
</div>
</body>
</html>