SILVA 16S database

[SoilRotifer (Mike Robeson)]

@AndreaC

I can't figure out which drop-down menus you are referring to.

I am referring to this drop-menu in the docs:

@AndreaC

I read in several posts that "If you're doing 16s sequencing rarely, or this is your first time, a pre-trained, full length classifer is fine." however, I notice significant differences between using a full database versus just one 16s.

Note this is specifically in reference to training nàive bayes classifiers, not necessarily Kraken 2 or other tools. In fact, I'd highly recommend reading the following papers about taxonomy assignments, and how to potentially improve them:

• Ziemski et al. 2021
• Kaehler et al. 2019
• Bokulich et al. 2018

@AndreaC

while for the data provided processed with silva database and qiime2, the results are very close to those I get through kraken2 and silva 16S, while if I try to replicate the analysis with qiime2 and the complete Silva database, I get % totally different.

@AndreaC

What database should I believe?

Short answer, who knows. It really depends on what questions you are trying to answer, and what makes sense given the environment your samples are from.

This all comes down to how the different versions of the databases are prepared. Without knowing how their database was curated (i.e. sequence quality and taxonomic nomenclature chosen) it is difficult to say which is "better". You can easily see how QIIME 2 SILVA databases were prepared by observing the provenance information, as it was made with RESCRIPt. We developed RESCRIPt, so that you can choose your own criteria for making and curating your own database. Thus, if you generally know how the other database was made, then you can try and replicate that processing with RESCRIPt / QIIME 2.