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

作者：LiMin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li · 发表于：Bioinformatics · 年份：2012 · DOI：10.1093/bioinformatics/bts565 · 被引用次数：12078 · 研究领域：Genomics and Phylogenetic Studies、Gene expression and cancer classification、Genomics and Rare Diseases

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.