Difference between revisions of "Usearch"
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[[Category:Software]] | [[Category:Software]] | ||
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|{{#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:citation|1}} <!--Enable Reference/Citation section --> | ||
|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
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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. | ||
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==Required Modules== | ==Required Modules== | ||
[[Modules|modules documentation]] | [[Modules|modules documentation]] | ||
===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
| − | {{#if: {{#var: exe}}|== | + | ==System Variables== |
| + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| + | <!--Additional--> | ||
| + | {{#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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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== | {{#if: {{#var: policy}}|==Usage Policy== | ||
| − | + | We have a 64-bit licensed USEARCH binary in the usearch/7.0.1001-64 module. | |
|}} | |}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
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</bibtex>--> | </bibtex>--> | ||
|}} | |}} | ||
| + | =Validation= | ||
| + | * Validated 4/5/2018 | ||
Latest revision as of 21:29, 6 December 2019
Description
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
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
