q2-fragment-insertion with silva v138

[Nicholas_Bokulich]

Hi @hsapers!

There has been some (long) discussion about how to build a SILVA 138 reference tree here:

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 …

The last post in that topic links to the instructions for building a reference tree (looks like the same steps that you linked to, plus a few additional steps).

@hsapers

I’m assuming that the reference tree should be calculated using the full length reference sequences and not just the targeted amplicon region?

Yes! definitely... using the full-length sequences for a more reliable phylogeny is the goal here.

@hsapers

Apologies if I’ve missed something straight forward.

Not at all... this is something that should probably be added to q2-fragment-insertion or another plugin at some point... up until now the reference phylogenies have mostly been built and distributed by others, but it would be ideal to democratize this process.

Good luck!