De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units.

ABSTRACT: Background. 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is optimal. A recent study suggested that a clustering method should be selected based on its ability to generate stable OTU assignments that do not change as additional sequences are added to the dataset. In contrast, we contend that the quality of the OTU assignments, the ability of the method to properly represent the distances between the sequences, is more important. Methods. Our analysis implemented six de novo clustering algorithms including the single linkage, complete linkage, average li

SUBMITTER: Westcott SL 

PROVIDER: S-EPMC4675110 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature