Ironing out the wrinkles in the rare biosphere through improved OTU clustering.

ABSTRACT: Deep sequencing of PCR amplicon libraries facilitates the detection of low-abundance populations in environmental DNA surveys of complex microbial communities. At the same time, deep sequencing can lead to overestimates of microbial diversity through the generation of low-frequency, error-prone reads. Even with sequencing error rates below 0.005 per nucleotide position, the common method of generating operational taxonomic units (OTUs) by multiple sequence alignment and complete-linkage clustering significantly increases the number of predicted OTUs and inflates richness estimates. We show that a 2% single-linkage preclustering methodology followed by an average-linkage clustering based on pairwise alignments more accurately predicts expected OTUs in both single and pooled template prepara

SUBMITTER: Huse SM 

PROVIDER: S-EPMC2909393 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature