DBH: A de Bruijn graph-based heuristic method for clustering large-scale 16S rRNA sequences into OTUs. (21st July 2017)

• Record Type: Journal Article
• Authors: Wei, Ze-Gang; Zhang, Shao-Wu
• Is Part Of: Journal of theoretical biology. Volume 425(2017)
• Page Start: 80
• Page End: 87
• Publication Date: 2017-07-21
• Subjects: de Bruijn graph -- Clustering -- Operational taxonomic units -- 16S rRNA -- Metagenomic; Biology -- Periodicals; Biological Science Disciplines -- Periodicals; Biology -- Periodicals; Biologie -- Périodiques; Theoretische biologie; Biology; Periodicals; 571.05
• DOI: 10.1016/j.jtbi.2017.04.019
• Languages: English
• ISSNs: 0022-5193

Abstract

Abstract: Recent sequencing revolution driven by high-throughput technologies has led to rapid accumulation of 16S rRNA sequences for microbial communities. Clustering short sequences into operational taxonomic units (OTUs) is an initial crucial process in analyzing metagenomic data. Although many heuristic methods have been proposed for OTU inferences with low computational complexity, they just select one sequence as the seed for each cluster and the results are sensitive to the selected sequences that represent the clusters. To address this issue, we present a de Bruijn graph-based heuristic clustering method (DBH) for clustering massive 16S rRNA sequences into OTUs by introducing a novel seed selection strategy and greedy clustering approach. Compared with existing widely used methods on several simulated and real-life metagenomic datasets, the results show that DBH has higher clustering performance and low memory usage, facilitating the overestimation of OTUs number. DBH is more effective to handle large-scale metagenomic datasets. The DBH software can be freely downloaded fromhttps://github.com/nwpu134/DBH.git for academic users.