What is your ‘species’ definition for species that lack matches in the reference database?
We generate Operational Taxonomic Units (OTUs) as part of our data processing pipeline. This is a taxonomy-free clustering approach based purely on how similar the sequences generated are to one another. The threshold at which the clusters are defined varies between assays because of the properties of different gene regions that are used. We treat each OTU as a species-level entity and attempt to make a taxonomic assignment for each but this will not always be possible at species level. All OTUs are included in estimates of diversity, regardless of whether we are able to assign a species label.
