Quality-score refinement of SSU rRNA gene pyrosequencing differs across gene region for environmental samples.

ABSTRACT: Due to potential sequencing errors in pyrosequencing data, species richness and diversity indices of microbial systems can be miscalculated. The "traditional" sequence refinement method is not sufficient to account for overestimations (e.g., length, primer errors, ambiguous nucleotides). Recent in silico and single-organism studies have revealed the importance of sequence quality scores in the estimation of ecological indices; however, this is the first study to compare quality-score stringencies across four regions of the SSU rRNA gene sequence (V1V2, V3, V4, and V6) with actual environmental samples compared directly to corresponding clone libraries produced from the same primer sets. The nucleic acid sequences determined via pyrosequencing were subjected to varying quality-score cutoffs

SUBMITTER: Bowen De Leon K 

PROVIDER: S-EPMC3391548 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature