CyberinfraV1, Ncbi, Checkpoint, bibRecord, 000361

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

Identifieur interne : 000361 ( Ncbi/Checkpoint ); précédent : 000360; suivant : 000362

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

Auteurs : Limin Fu ; Beifang Niu ; Zhengwei Zhu ; Sitao Wu ; Weizhong Li

Source :

Bioinformatics [ 1367-4803 ] ; 2012.

RBID : PMC:3516142

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.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516142

DOI: 10.1093/bioinformatics/bts565
PubMed: 23060610
PubMed Central: 3516142

Affiliations:

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PMC:3516142

Le document en format XML

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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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<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>
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<email>liwz@sdsc.edu</email>
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<p><bold>Supplementary information:</bold>
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CD-HIT: accelerated for clustering the next-generation sequencing data

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

Source :

Abstract

Links toward previous steps (curation, corpus...)

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Le document en format XML

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Pour générer des pages wiki