What is the proper input for "qiime fragment-insertion sepp" plugin if I want to build a gg2 tree?

[Nicholas_Bokulich]

Hi @jjj33 ,
I think your query is answered here:

SEPP reference databases for Greengenes2

Hi @Uni, Thank you for the kind words! Fragment placement in Greengenes2 uses an improved algorithm called DEPP. For 2022.10 we placed ~20M V4 ASVs, which can be readily used. For non V4 data, we do not yet have a means to place fragments but we are working on getting the steps described in a tutorial. For these data, one viable path forward would be to use the non-v4-16s action which performs closed reference recruitment to the backbone, and then to use the 2022.10.phylogeny.id.nwk.qza phylog…

Good luck!