CD-HIT: accelerated for clustering the next-generation sequencing data
Identifieur interne : 000361 ( Ncbi/Checkpoint ); précédent : 000360; suivant : 000362CD-HIT: accelerated for clustering the next-generation sequencing data
Auteurs : Limin Fu ; Beifang Niu ; Zhengwei Zhu ; Sitao Wu ; Weizhong LiSource :
- Bioinformatics [ 1367-4803 ] ; 2012.
Abstract
Url:
DOI: 10.1093/bioinformatics/bts565
PubMed: 23060610
PubMed Central: 3516142
Affiliations:
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PMC:3516142Le document en format XML
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<author><name sortKey="Fu, Limin" sort="Fu, Limin" uniqKey="Fu L" first="Limin" last="Fu">Limin Fu</name>
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<author><name sortKey="Niu, Beifang" sort="Niu, Beifang" uniqKey="Niu B" first="Beifang" last="Niu">Beifang Niu</name>
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<author><name sortKey="Zhu, Zhengwei" sort="Zhu, Zhengwei" uniqKey="Zhu Z" first="Zhengwei" last="Zhu">Zhengwei Zhu</name>
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<author><name sortKey="Wu, Sitao" sort="Wu, Sitao" uniqKey="Wu S" first="Sitao" last="Wu">Sitao Wu</name>
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<author><name sortKey="Li, Weizhong" sort="Li, Weizhong" uniqKey="Li W" first="Weizhong" last="Li">Weizhong Li</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">CD-HIT: accelerated for clustering the next-generation sequencing data</title>
<author><name sortKey="Fu, Limin" sort="Fu, Limin" uniqKey="Fu L" first="Limin" last="Fu">Limin Fu</name>
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<author><name sortKey="Niu, Beifang" sort="Niu, Beifang" uniqKey="Niu B" first="Beifang" last="Niu">Beifang Niu</name>
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<author><name sortKey="Zhu, Zhengwei" sort="Zhu, Zhengwei" uniqKey="Zhu Z" first="Zhengwei" last="Zhu">Zhengwei Zhu</name>
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<author><name sortKey="Wu, Sitao" sort="Wu, Sitao" uniqKey="Wu S" first="Sitao" last="Wu">Sitao Wu</name>
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<author><name sortKey="Li, Weizhong" sort="Li, Weizhong" uniqKey="Li W" first="Weizhong" last="Li">Weizhong Li</name>
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<series><title level="j">Bioinformatics</title>
<idno type="ISSN">1367-4803</idno>
<idno type="eISSN">1367-4811</idno>
<imprint><date when="2012">2012</date>
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<front><div type="abstract" xml:lang="en"><p><bold>Summary:</bold>
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.</p>
<p><bold>Availability:</bold>
<ext-link ext-link-type="uri" xlink:href="http://cd-hit.org">http://cd-hit.org</ext-link>
.</p>
<p><bold>Contact:</bold>
<email>liwz@sdsc.edu</email>
</p>
<p><bold>Supplementary information:</bold>
<ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/cgi/content/full/bts565/DC1">Supplementary data</ext-link>
are available at <italic>Bioinformatics</italic>
online.</p>
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<name sortKey="Zhu, Zhengwei" sort="Zhu, Zhengwei" uniqKey="Zhu Z" first="Zhengwei" last="Zhu">Zhengwei Zhu</name>
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