alexa CD-HIT: accelerated for clustering the next-generation sequencing data.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Data Mining in Genomics & Proteomics

Author(s): Fu L, Niu B, Zhu Z, Wu S, Li W

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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: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
This article was published in Bioinformatics and referenced in Journal of Data Mining in Genomics & Proteomics

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