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Bioinformatics. 2012 Dec 1;28(23):3150-2. doi: 10.1093/bioinformatics/bts565. Epub 2012 Oct 11.

CD-HIT: accelerated for clustering the next-generation sequencing data.

Author information

1
Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093, USA.

Abstract

SUMMARY:

CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequencing data produced by the next-generation sequencing technologies, we have developed a new CD-HIT program accelerated with a novel parallelization strategy and some other techniques to allow efficient clustering of such datasets. Our tests demonstrated very good speedup derived from the parallelization for up to ∼24 cores and a quasi-linear speedup for up to ∼8 cores. The enhanced CD-HIT is capable of handling very large datasets in much shorter time than previous versions.

AVAILABILITY:

http://cd-hit.org.

CONTACT:

liwz@sdsc.edu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
23060610
PMCID:
PMC3516142
DOI:
10.1093/bioinformatics/bts565
[Indexed for MEDLINE]
Free PMC Article

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