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cmd_cluster_otus.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>
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<title>
allpairs_global command
</title>
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</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;"/>
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Docs home
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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_otus command
</h1>
<p class="ManText">
<b>
See also
<br/>
</b>
<a href="uparse_pipeline.html">
OTU / denoising pipeline
</a>
<br/>
<a href="tutorials.html">
Tutorials with data, scripts, and excercises with solutions
</a>
<br/>
<a href="otus.html">
Defining and interpeting OTUs
</a>
<br/>
<b>
</b>
<span class="Text">
<a href="otu_bench.html">
OTU benchmark results
</a>
</span>
<br/>
<b>
</b>
<a href="cmd_otutab.html">
Making an OTU table (otutab command)
</a>
<br/>
<b>
</b>
<a href="faq_uparse_or_unoise.html">
Should I use UPARSE or UNOISE?
</a>
<b>
<br/>
</b>
<span class="ManText">
<br/>
The cluster_otus command performs 97% OTU clustering using the
<a href="uparseotu_algo.html">
UPARSE-OTU algorithm
</a>
.
</span>
</p>
<p class="ManText">
Chimeras are filtered by this command. This chimera filtering is much better than using UCHIME so I do not recommend using reference-based chimera filtering as a post-processing step
(except perhaps for manual review), because false positives are common.
</p>
<p class="ManText">
For most purposes, I consider 97% OTU clustering obsolete. It is better to use the
<a href="cmd_unoise3.html">
unoise command
</a>
to recover the full set of biological sequences in the reads. These are also valid OTUs; I call them "ZOTUs" for zero-radius OTUs, to emphasize this. See
<a href="otus.html">
defining and interpreting OTUs
</a>
and the
<a href="citation.html">
UNOISE paper
</a>
for further discussions.
</p>
<p>
<span class="ManText">
Input to cluster_otus is a FASTA file containing
<a href="readqualfiltering.html">
quality filtered
</a>
,
<a href="global_trimming.html">
globally trimmed
</a>
and
<a href="upp_derep.html">
dereplicated
</a>
reads from a marker gene amplicon sequencing experiment, e.g. 16S or ITS. It is generally recommended that
<a href="singletons.html">
singleton reads should be discarded
</a>
.
</span>
</p>
<p>
<span class="ManText">
See
<a href="uparse_pipeline.html">
OTU / denoising pipeline
</a>
for discussion of how to prepare reads before clustering. It is
<strong>
<span class="auto-style1">
strongly recommended
</span>
</strong>
that you follow the pipeline recommentations, otherwise the accuracy of the OTUs will probably be compromised.
</span>
</p>
<p>
<span class="ManText">
Input sequence labels must have
<a href="size_annot.html">
size annotations
</a>
giving the abundance of the unique sequence. Size annotations are generated by the -sizeout option of clustering commands; typically
<a href="cmd_fastx_uniques.html">
fastx_uniques
</a>
is used.
</span>
</p>
<p>
<span class="ManText">
The -minsize option can be used to specify a minimum abundance. Default value is 2, which
<a href="singletons.html">
discards singleton unique sequences
</a>
.
</span>
</p>
<p>
<span class="ManText">
The identity threshold is fixed at 97%. See
<a href="otus.html">
defining and intepreting OTUs
</a>
for discussion. See
<a href="uparse_otu_radius.html">
UPARSE OTU radius
</a>
for making OTUs at different identities.
</span>
</p>
<p>
<span class="ManText">
The -
<a href="opt_otus.html">
otus
</a>
option specifies a FASTA output file for the OTU representative sequences. By default, OTUs labels are taken from the input file, with
<a href="size_annot.html">
size annotations
</a>
stripped.
</span>
</p>
<p>
<span class="ManText">
The -
<a href="opt_relabel.html">
relabel
</a>
option specifies a string that is used to re-label OTUs. If -relabel xxx is specified, then the labels are xxx followed by 1, 2 ... up to the number of OTUs. OTU identifiers in the labels is required for making an OTU table with the
<a href="cmd_otutab.html">
otutab command
</a>
.
</span>
</p>
<p>
<span class="ManText">
The -
<a href="opt_uparseout.html">
uparseout
</a>
option specifies a tabbed text output file documenting how the input sequences were classified.
</span>
</p>
<p>
<span class="ManText">
The -uparsealnout option species a text file containing a human-readable alignment of each query sequence to its
<a href="uparseref_algo.html">
UPARSE-REF
</a>
model.
</span>
</p>
<p>
<span class="ManText">
<a href="parsimony_params.html">
Parsimony score options
</a>
are supported.
</span>
</p>
<p>
<span class="ManText">
<a href="aln_params.html">
Alignment parameters
</a>
and
<a href="aln_heuristics.html">
heuristics
</a>
are supported.
</span>
</p>
<p>
<span class="ManText c2">
Example
</span>
</p>
<p>
<span class="ManCode">
usearch -cluster_otus uniques.fa -otus otus.fa -uparseout uparse.txt -relabel Otu
<br/>
</span>
</p>
</div>
</div>
</body>
</html>