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long_v4.html
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long_v4.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"/>
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<title>
allpairs_global command
</title>
<link href="stylesx.css" rel="stylesheet" type="text/css"/>
<style type="text/css">
body.c4 {background-color:#c0c0c0;}
div.c3 {position:absolute; top:45px; left:20px; width:830px; background-color:#ffffff; border-width:10px; border-style:solid;border-color:white;}
span.c2 {font-weight: bold}
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<div class="ManText" style="left:20px; position: absolute; left:135px; width:695px; background-color:white; padding:10px">
<h1>
Long overlaps are not needed, so 2x250 can do better than V4
</h1>
<p class="ManText">
Some people have suggested that the almost complete overlap obtained with 2x250 V4 is a good strategy because it gives the best error correction. I disagree. In my opinion, for most applications the reduction in error rate is not dramatic and does not compensate for the improved phylogenetic resolution you get with longer sequences.
</p>
<p class="ManText">
Using
<a href="/uparse/">
UPARSE
</a>
or
<a href="unoise_algo.html">
UNOISE
</a>
gives very accurate OTUs regardless of the overlap length. As a proof of concept, you can generally get good OTUs if you throw away forward reads for V4 and use reverse (R2) reads only, despite the lower quality of the R2s. I therefore recommend sequencing the longest possible amplicon that will give a minimum overlap of around 20 to 30 nt.
<br/>
</p>
</div>
</div>
</body>
</html>