How to build a GTDB-based phylogenetic tree using fragment-insertion method?

[jjj33 (jiang yuesong)]

Hi everyone,

I'm pretty interested in how to build a GTDB-based phylogenetic tree using the fragment-insertion method. I haven't found any posts related to building a GTDB-based tree. Is there already any available artifact? Also, can I use the following command to achieve this (if so, what's the input material for parameter --i-reference-database)?

qiime fragment-insertion sepp
--i-representative-sequences rep-seqs.qza
--i-reference-database ?.qza
--o-tree tree.qza
--o-placements tree_placements.qza
--p-threads 8

Thanks in advance!

Jason

[Nicholas_Bokulich]

Hi @jjj33 ,
The topic below has some relevant discussion and links for how to generate a custom SEPP database:

Trouble generating SeppReferenceDatabase qza

Hi! I'm new to qiime2, so I'm not sure if I'm having problems because I couldn't find instructions for importing/creating a SeppReferenceDatabase. Goal: Use a customized subset of Silva 138 NR99 for sepp fragment insertion. What I've done: Using arb, exported the aligned fasta for the high quality seqs I want to use, after trimming to just the relevant 16S region, and exported the corresponding tree. Followed Siavash's steps to clean up the tree, resolve polytomies, and re-estimate branch …

As far as I know, it is a complicated process and I do not know of anyone other than the original SEPP/fragment-insertion developers who have managed to create a working SEPP reference, just so you know what you are getting yourself into...

Good luck!