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cluster_sizes.html
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allpairs_global command
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<h1>
propagating cluster sizes
</h1>
<span class="ManText">
<br/>
In some applications, sequences are clustered in two or two or more passes by different USEARCH commands and/or by other programs. Sometimes, the size of a cluster is required in terms of the number of sequences that were provided to the first stage of a pipeline. For example, 16S reads might
<a href="dereplication.html">
dereplicated
</a>
then clustered into OTUs by
<a href="cmd_cluster_otus.html">
cluister_otus
</a>
.
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<p>
<span class="ManText">
To handle multi-step clustering, USEARCH provides a mechanism to propagate cluster
<a href="size_annot.html">
size annotations
</a>
. If the -sizein option is specified, input sequences are required to have a size annotation. If the -sizeout option is specified, size annotations are added to the output labels. If both -sizein and -sizeout are given, then the output size for a cluster takes into account the input sizes.
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Typical use is:
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<p>
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1. First clustering or dereplication step in the pipeline uses -sizeout.
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2. Subsequent clustering steps use both -sizein and -sizeout.
<br/>
<br/>
If another program is used before the first USEARCH step, then it is up to you to write scripts to produce
<a href="size_annot.html">
size annotations
</a>
for USEARCH.
<br/>
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