Difference between revisions of "Usearch"

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{{#if: {{#var: citation}}|==Citation==
 
{{#if: {{#var: citation}}|==Citation==
 
If you publish research that uses {{#var: app}} you have to cite it as follows:
 
If you publish research that uses {{#var: app}} you have to cite it as follows:
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<pre>
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Edgar, Robert C. - Search and clustering orders of magnitude faster than BLAST
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Bioinformatics , 2010
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Author : Edgar, Robert C.
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Title : Search and clustering orders of magnitude faster than BLAST
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Publication : Bioinformatics
 +
Date : 2010
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</pre>
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journal = {Bioinformatics}  
 
journal = {Bioinformatics}  
 
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Revision as of 18:13, 25 October 2011

Description

{{{name}}} website  
USEARCH is a unique high-throughput sequence analysis tool. It is a distributed as single binary program that implements a suite of algorithms comparable to BLASTN, BLASTP, BLASTX, BLASTCLUST, CD-HIT, CD-HIT-EST, CD-HIT-2D, CD-HIT-EST-2D, CD-HIT-OTU, CD-HIT-454, ChimeraSlayer, Perseus, RAPsearch and more. It supports a rich set of sequence matching options, including E-values, identity, coverage (fraction of query or target sequence covered by the alignment) and maximum gap length, and a range of output file formats including FASTA, BLAST-like, user-defined tabbed text and a native format designed for clustering applications. Supported alignment styles include local (gapped and ungapped), like BLAST, and global, which is most often used in clustering applications. User-settable parameters allow tuning of substitution scores, gap penalties and Karlin-Altschul statistics. Template:App Location

Running the application using modules

To use usearch with the environment modules system at HPC the following commands are available:

Get module information for usearch:

$module spider usearch

Load the default application module:

$module load usearch

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_USEARCH_DIR - directory where usearch is located.


Usage policy

Our license only allows the usage of a 32-bit binary for teaching and non-profit (academic research) purposes. If your use falls outside of these categories please procure a license from the author.


Citation

If you publish research that uses usearch you have to cite it as follows:

Edgar, Robert C. - Search and clustering orders of magnitude faster than BLAST
Bioinformatics , 2010
Author : Edgar, Robert C.
Title : Search and clustering orders of magnitude faster than BLAST
Publication : Bioinformatics
Date : 2010