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J Microbiol Methods. 2013 Sep;94(3):347-55. doi: 10.1016/j.mimet.2013.07.004. Epub 2013 Jul 28.

MSClust: A Multi-Seeds based Clustering algorithm for microbiome profiling using 16S rRNA sequence.

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College of Automation, Northwestern Polytechnical University, 710072 Xi'an, China.


Recent developments of next generation sequencing technologies have led to rapid accumulation of 16S rRNA sequences for microbiome profiling. One key step in data processing is to cluster short sequences into operational taxonomic units (OTUs). Although many methods have been proposed for OTU inferences, a major challenge is the balance between inference accuracy and computational efficiency, where inference accuracy is often sacrificed to accommodate the need to analyze large numbers of sequences. Inspired by the hierarchical clustering method and a modified greedy network clustering algorithm, we propose a novel multi-seeds based heuristic clustering method, named MSClust, for OTU inference. MSClust first adaptively selects multi-seeds instead of one seed for each candidate cluster, and the reads are then processed using a greedy clustering strategy. Through many numerical examples, we demonstrate that MSClust enjoys less memory usage, and better biological accuracy compared to existing heuristic clustering methods while preserving efficiency and scalability.


16S rRNA reads; Clustering algorithms; Next-generation sequencing; Operational taxonomic unit (OTU); Seeds-selection

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