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USEARCH

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.

Note, only a 32-bit binary is available. If you require a 64-bit binary the software will have to be purchased from the author.

Environment Modules

Run module spider usearch to find out what environment modules are available for this application.

Environment Variables

  • HPC_USEARCH_DIR - installation directory
  • HPC_USEARCH_BIN - executable directory

Additional Usage Information

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

Citation

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

Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26(19), 2460–2461. https://doi.org/10.1093/bioinformatics/btq461

Categories

biology, alignment, sequencing