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cmd_sintax.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;}
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}
div.c1 {position:absolute; top:10px; left:20px; width:850px; height:60px;}
.TopButtonPara { color:white; background-color:rgb(50,100,150); border-color:rgb(50,100,150); font-family:Arial, Helvetica, sans-serif; font-weight:normal; font-size:9pt; text-align:center; border-width:4px; border-style:solid; }
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a.TopButton:link { text-decoration:none; }
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a.SideButton:link { text-decoration:none; }
a.SideButton:visited { text-decoration:none; }
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>
sintax command
<span class="ManText">
<b>
<a href="videos.html">
<img alt="" height="56" src="video_lectures_tax.png" style="float: right" width="167"/>
</a>
</b>
</span>
</h1>
<br/>
<span class="ManText">
<b>
See also
<br/>
</b>
<a href="sintax_downloads.html">
SINTAX reference data downloads
</a>
<br/>
<a href="faq_tax_db.html">
Which taxonomy database should I use?
</a>
<br/>
<b>
</b>
<a href="sintax_algo.html">
SINTAX algorithm
</a>
<br/>
<a href="DELETE_URL">
makeudb_sintax command
</a>
<br/>
<a href="sintax_species.html">
Can SINTAX predict species?
</a>
<br/>
<a href="cmd_sintax_summary.html">
sintax_summary command
</a>
<br/>
<a href="cvi.html">
Cross-validation by identity
</a>
<br/>
<a href="tax_conf.html">
Taxonomy confidence measures
</a>
<br/>
<b>
<br/>
</b>
The sintax command uses the
<a href="sintax_algo.html">
SINTAX algorithm
</a>
to predict taxonomy for query sequences
in FASTA or FASTQ format.
<br/>
<br/>
You can use the
<a href="cmd_sintax_summary.html">
sintax_summary command
</a>
to get a tabbed text file for making figures.
</span>
<p>
<span class="ManText">
The search database must have
<a href="tax_annot.html">
taxonomy annotations
</a>
. The
<a href="DELETE_URL">
makeudb_sintax command
</a>
can be used to create a
<a href="udb_files.html">
UDB database
</a>
, which is faster to load. See
<a href="sintax_downloads.html">
SINTAX downloads
</a>
page for available reference files in FASTA format. See also
<a href="faq_tax_db.html">
Which database should I use?
</a>
</span>
</p>
<p>
<span class="ManText">
<a href="tax_pred.html">
Taxonomy predictions
</a>
with
<a href="tax_conf.html">
bootstrap confidence
</a>
values are written to the -tabbedout file. The first three fields are (1) query sequence label, (2) prediction with
bootstrap values and (3) strand. If the -sintax_cutoff option is given then predictions are written a second time after applying the confidence threshold, keeping only ranks with high enough confidence. On V4 reads, using a cutoff of 0.8 gives predictions with similar accuracy to RDP at 80% bootstrap cutoff.
</span>
</p>
<p>
<span class="ManText">
The
<a href="opt_strand.html">
strand option
</a>
must be specified.
</span>
</p>
<p>
<span class="ManText">
<a href="multithreading.html">
Multithreading
</a>
is supported.
</span>
</p>
<p>
<span class="ManText c3">
Example
</span>
</p>
<p>
<span class="ManCode">
usearch -sintax reads.fastq -db 16s.udb -tabbedout reads.sintax
\
<br/>
-strand both -sintax_cutoff 0.8
<br/>
</span>
</p>
<span class="ManText">
<br/>
<strong>
References (please cite)
</strong>
<br/>
<span class="ManText">
R.C. Edgar (2016), SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences,
<a href="https://doi.org/10.1101/074161">
https://doi.org/10.1101/074161
</a>
</span>
<span style="font-size:9pt; line-spacing:9pt;">
<br/>
<i>
• SINTAX taxonomy prediction algorithm
</i>
</span>
<span style="font-size:9pt; line-spacing:9pt;">
<br/>
<i>
• Fast and simple method, accuracy comparable to RDP Classifier
</i>
</span>
<br/>
<br/>
<span class="ManText">
R.C. Edgar (2018), Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences,
<a href="https://doi.org/10.7717/peerj.4652">
PeerJ 6:e4652
</a>
</span>
<span style="font-size:9pt; line-spacing:9pt;">
<br/>
<i>
• Cross-validation by identity, novel benchmark strategy enabling realistic accuracy estimates
</i>
</span>
<span style="font-size:9pt; line-spacing:9pt;">
<br/>
<i>
• Genus accuracy of best methods is 50% on V4 sequences
</i>
</span>
<span style="font-size:9pt; line-spacing:9pt;">
<br/>
<i>
• Recent algorithms do not improve on RDP Classifier or SINTAX
</i>
</span>
<br/>
<br/>
<span class="ManText">
R.C. Edgar (2018), Taxonomy annotation and guide tree errors in 16S rRNA databases,
<a href="https://doi.org/10.7717/peerj.5030">
PeerJ 6:e5030
</a>
</span>
<span style="font-size:9pt; line-spacing:9pt;">
<br/>
<i>
• Approx. one in five SILVA and Greengenes taxonomy annotations are wrong
</i>
</span>
<span style="font-size:9pt; line-spacing:9pt;">
<br/>
<i>
• SILVA and Greengenes trees have pervasive conflicts with type strain taxonomies
</i>
</span>
<br/>
<br/>
</span>
</div>
</div>
</body>
</html>