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. 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

Limin Fu  1 , Beifang Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li
Affiliations

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

Limin Fu et al. Bioinformatics. .

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.

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Figures

Fig. 1.
Fig. 1.
Evaluation of CD-HIT parallelization: computational time speedup with respect to the number of used CPU cores
See this image and copyright information in PMC

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