I have been using Mothur for a few years now to analyze V4 and V9 18S rRNA data for metazoan zooplankton communities. Current trends in the metabarcoding field are shifting towards analyses of Exact Sequence Variance (ESVs) instead of clustering sequences at similarity thresholds into OTUs. I was wondering if the “unique sequences” that are identified in Mothur after quality control, filtering, and chimera detection are analogous to ESVs that are generated using pipelines such as DADA2 (Callahan et al., 2016 DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods 13(7):581-587. doi:10.1038/nmeth.3869). It seems the DADA2 runs sequences through more stringent quality control to ensure detection of PCR errors, fewer false positives for taxonomic identifcations, and low error rates.
I have been classifying the unique sequences identified after running my Illumina data through the Mothur pipeline against a proprietary DNA reference database to get species level identications for zooplankton. I’m curious to know your thoughts on if “unique seqs” would be accepted at ESVs by the scientific community or if I would have to use the DADA2 pipeline for this purpose.