I have been working on a 16S-seq microbiome abundance experiment analysis for quite some time and I still can't decide which database I should use to assign taxonomy. As a background, I recently switched over from QIIME to DADA2 and I am deciding between SILVA, RDP, and the Genome Taxonomy Database (GTDB). I've never heard of GTDB before DADA2 but this database did a great job at annotating most of my ASVs all the way down to bacterial genera.
My question is has anyone worked with GTDB before and can they speak to its accuracy? Mine did a good job of recapitulating the results from QIIME with Greengenes as the database but I'm still not 100% sold because it seems like SILVA and RDP are the most popular at the moment.
Any suggestions welcome, thanks.