Difference between revisions of "Usearch"

From UFRC
Jump to navigation Jump to search
m (Text replace - "<!-- ######## Template Configuration ######## --> <!--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 prod)
m (Text replace - "<!--Choose sections to enable - OPTIONAL--> |{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->" to "")
Line 10: Line 10:
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
|{{#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: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 -->

Revision as of 17:53, 10 August 2012


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.

Available Versions

  • 5.0.151 and 5.1.221 (EL5).
  • 5.2.32 (EL6).

Note: only 32-bit binaries are available limiting the memory use to less then 4GB. If a 64-bit binary is needed it will have to be purchased from the author.

Required Modules

modules documentation

Serial

  • usearch


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