Reasons to use Greengenes / Silva databases instead of NCBI Blast?


I’ve been wondering, is there any reasons why QIIME2 seems to be favoring the use of Greengenes and Silva databases instead of NCBI Blast database?

I had a sample that was analysed using Greengenes database, that was missing some bacteria (we expected them to be in that sample). When I re-analyse the OTUs using NCBI Blast database, the database was able to recognise the bacteria.

I also read a paper that compares the three databases and found NCBI Blast database to be the most comprehensive.

So I’m wondering why is it that Greengenes and Silva databases are mentioned and used so much more often in Qiime2 docs? There must be a reason for that, right? What is it that I’m missing? :slightly_smiling_face: FYI, I’m new to microbiome analysis so I’d appreciate your insights on this.

Many thanks :slight_smile:

Hi @fgara,

There was some discussion about this not that long ago:



Hi Justine, thank you so much! :slight_smile:

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