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

LiMin Fu; Beifang Niu; Zhengwei Zhu; Sitao Wu; Weizhong Li

doi:10.1093/bioinformatics/bts565

October 11, 2012BioinformaticsOpen Access

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

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Key Points

To accelerate the CD-HIT sequence clustering algorithm to effectively handle the high data throughput produced by next-generation sequencing platforms.
Optimized the CD-HIT algorithm architecture to improve computational throughput and reduce memory consumption for ultra-large sequence collections.
Implemented algorithmic improvements tailored specifically to cluster short and high-volume sequencing reads.
Substantially reduced execution runtime, facilitating the clustering of tens of millions of sequencing reads.
Maintained sequence clustering fidelity while minimizing memory bottlenecks associated with massive next-generation sequencing datasets.

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Software evaluation demonstrates accelerated sequence clustering for next-generation sequencing data, highlighting scalable analysis for massive genomic datasets.

Abstract

Supplementary data are available at Bioinformatics online.

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Fu et al. (2012) studied this question.

synapsesocial.com/papers/69d6c7b275cae9790bed8b35 https://doi.org/10.1093/bioinformatics/bts565

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

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Abstract

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

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