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

[jjj33 (jiang yuesong)]

Hi all,

Thanks in advance to those who can help me out. I've read through the "Parkinson’s Mouse Tutorial" and tried to build a gg2-based phylogenetic tree using the "qiime fragment-insertion sepp" plugin:

qiime fragment-insertion sepp
--i-representative-sequences rep-seqs.qza
--i-reference-database 2024.09.backbone.full-length.fna.qza
--o-tree tree.qza
--o-placements tree_placements.qza
--p-threads 8

And I realized that "2024.09.backbone.full-length.fna.qza" is not the proper input. I noticed there is a post and a corresponding repository that contains lots of QIIME 2 compatible artifacts:

I believe there's a ready-to-use input file for parameter "--i-reference-database" (or maybe not?). Can anyone kindly point out which file I should use in the repo to run the "qiime fragment-insertion sepp" plugin?

Jason

[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!

[callaban (Celeste Allaband)]

Hi Jason and @Nicholas_Bokulich,

There is a post about using GG2 with SEPP here in conjunction with @wasade.

"Given these observations, it now seems viable to use SEPP with Greengenes2 to obtain a phylogeny from arbitrary amplicon sequence variants. A Greengenes2 2022.10 reference compatible with q2-fragment-insertion can be obtained from the Greengenes2 FTP."

-Celeste