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A methodological shift in how research teams investigate microbial diversity has been introduced by advances in the analysis of amplicon sequence datasets has occurred, moving from sequence identity-based clustering to denoising techniques. Although denoising methods have several inherent characteristics that make them more effective than clustering-based strategies, questions remain as to the impact that these pipelines have on the ecological patterns being investigated, particularly in comparison to other methodological choices made when processing data and computing diversity indices. We compared the respective effects of two commonly used techniques, including DADA2 vs. Mothur on 16S rRNA gene amplicon datasets, and compared such findings to the rarefaction of the community table and the OTU identity threshold on the ecological signals identified, comparing the ecological parameters found. We used a survey that collected freshwater invertebrate gut and environmental samples in six rivers in the southeastern United States.
Source link: https://doi.org/10.1371/journal.pone.0264443
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