IHi @SaraGajas ,
I would avoid setting the taxonomic classification this high, leave this at the default (0.8
). Otherwise you'll end up with very few taxonomic classifications or only upper-level classifications (i.e. class, order...). For more details I'd recommend reading the Taxonomy Overview and the q2-feature-classifier paper.
Remember these classifiers are not necessarily returning only the best / top hit. Often you'll have equivalent "hits" across several members in the databases. In this case a consensus taxonomy will be returned. That is, both vsearch and BLAST+, as implemented in QIIME 2, will perform database searching, followed by LCA (lowest common ancestor) taxonomy consensus assignment.
They are all good, which is why we offer these as options, see the overview link. Personally, I prefer to use naïve bayes classifier through sklearn.
-Mike