Usearch

From UFRC
Revision as of 02:03, 10 August 2012 by Moskalenko (talk | contribs) (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==")
Jump to navigation Jump to search

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.

Execution Environment and 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