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

ABSTRACT: 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.http://cd-hit.org.liwz@sdsc.eduSupplementary data are available at Bioinformatics online.

SUBMITTER: Fu L

PROVIDER: S-EPMC3516142 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

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

Fu Limin L Niu Beifang B Zhu Zhengwei Z Wu Sitao S Li Weizhong W

Bioinformatics (Oxford, England) 20121011 23

<h4>Summary</h4>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 de ...[more]

PMID: 23060610

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