In bioinformatics databases play an important role in the results, whether chimera detection or OTUs assignment (16S metagenomics). In your experience, which databases have a better relation number/quality of sequences?
Ezbiocloud
Silva
RDP
Greengenes
Do you know a paper that deals this topic?
Silva includes well annotated sequences from both 16s and 18s genes, so if by your method (filtering for example) you expect prokaryotes and eukaryotes then that is (probably) your only choice. All the rest are prokaryotic-only databases of sequences (16s). Some people just don't realize that there are eukaryotes really small (check for example Ostreococcus), so please consider that issue. Thus, in order to get a complete picture of your microbial community I would recommend Silva.
I agree with Salvador, SILVA is a standard and curated reference dataset for taxonomy and it is recently upgraded. An article discussing differences pros and cons of different reference databases for 16S at: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3501-4
Very interesting article Howard. Thanks for the link -- I missed that one. However, they conclude that the NCBI database of rRNA sequences is the best for comparing metagenomics datasets. I kind of disagree with them.. I will look for the details.
Best regards.
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