SILVA vs GreenGenes


I’ve noticed that the GreenGenes database hasn’t been updated since 2013, so is SILVA the preferred database in 2017?


Well, it depends. For alignments, SILVA has always been the preferred reference. For taxonomy, it’s mostly a matter of taste and environment. The RDP also makes a nice reference taxonomy. I’m not sure that the updates really change much, which is part of the reason I’ve been slow to update our SILVA reference and why the RDP doesn’t get updated all that frequently. But it does seem like the greengenes development has stalled.


Okay, I guess I’m unclear as to the difference between alignment and taxonomy. I’ll have to read up on that.

Alignment is done at align.seqs - you can find a discussion of our reasons for preferring SILVA at

Your sequences have to be aligned to calculate pairwise distances and do OTU/de novo clustering

Classification is alignment-inependent and is the process of pegging a name on to a sequence. There's about 5 different classification schemes that vary as a matter of taste and underlying database composition.