How to choose between full-length Greengenes or SILVA for 16s rRNA V1-V2 analysis with qiime2 pipeline?

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Hello Kida,

Welcome to the Qiime2 forums! :qiime2:

This is a great question. First, you can choose a denoising/clustering pipeline like deblur or DADA2, then select a database later.

The database should match your amplicons, like Greengenes for 16S or Unite for ITS.
Some classifiers are customized for a region, like V4 or V1-V2 like you have.

If you want to use Greengenes2 for V1-V2, use the qiime greengenes2 non-v4-16s action.
Or go for something simple and classic like classify-consensus-vsearch

Human stool is well-studied, so any database should work well! :computer:

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