Using both Silva and Greengenes in the analysis?

Hi all,

I just read a couple of papers ( & and could not understand why they used both databases in their analysis.

The MiSeq standard operating protocol was followed with the following modifications: after sequences were assembled, sequences that had any ambiguous bases or were longer than 275 bp were removed; sequences that passed this initial screening process were aligned to the Silva reference database (Release 123); …after chimera removal, the Wang method was used for taxonomic classification of samples with the greengenes reference database (August 2013 version)

Obviously that will not interfere with OTU classification. But why use Silva for alignment and not use either one for the whole analysis?


SILVA is the preferred database for sequence alignments. There really is no exception to that.

What database one uses for classification is a matter of personal preference. The options are RDP, SILVA, or greengenes. The only modification from teh SOP in that sentence is the use of greengenes instead of RDP - and that’s pretty reasonable.