Difference between revisions of "Usearch"

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[[Category:Software]]
 
[[Category:Software]]
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{|<!--Main settings - REQUIRED-->
<!--Edit definitions of the variables used in template calls
 
Required variables:
 
app - lowercase name of the application e.g. "amber"
 
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
Optional variables:
 
INTEL - Version of the Intel Compiler e.g. "11.1"
 
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
-->
 
{|
 
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|usearch}}
 
|{{#vardefine:app|usearch}}
 
|{{#vardefine:url|http://www.drive5.com/usearch/}}
 
|{{#vardefine:url|http://www.drive5.com/usearch/}}
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|{{#vardefine:citation|1}} <!--Enable Reference/Citation section -->
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
<!--Choose sections to enable - OPTIONAL-->
 
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
 
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
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|{{#vardefine:policy|1}} <!--Enable policy section -->
 
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 
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|}
 
|}
 
<!-- ########  Template Body ######## -->
 
<!-- ########  Template Body ######## -->
 
<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
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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.
 
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.
<!--Location-->
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<!--Modules-->
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
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==Required Modules==
<!-- -->
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[[Modules|modules documentation]]
{{#if: {{#var: mod}}|==Running the application using modules==
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===Serial===
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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*{{#var:app}}
{{#if: {{#var: exe}}|==How To Run==
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 +
<!--Additional-->
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{{#if: {{#var: exe}}|==Additional Information==
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
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{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
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We have a 64-bit licensed USEARCH binary in the usearch/7.0.1001-64 module.
 +
|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==
 
WRITE PERFORMANCE TESTING RESULTS HERE|}}
 
WRITE PERFORMANCE TESTING RESULTS HERE|}}
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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:
 +
<pre>
 +
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
 +
</pre>
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<!--
 
<bibtex>
 
<bibtex>
 
@article{Edgar12082010,
 
@article{Edgar12082010,
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journal = {Bioinformatics}  
 
journal = {Bioinformatics}  
 
}
 
}
</bibtex>
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</bibtex>-->
 
|}}
 
|}}
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=Validation=
 +
* Validated 4/5/2018

Latest revision as of 21:29, 6 December 2019

Description

usearch 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.

Required Modules

modules documentation

Serial

  • usearch

System Variables

  • HPC_USEARCH_DIR - installation directory


Usage Policy

We have a 64-bit licensed USEARCH binary in the usearch/7.0.1001-64 module.


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

Validation

  • Validated 4/5/2018