Update `SeppReferenceTree` to SILVA 138.1

[crusher083 (Valentyn Bezshapkin)]

Hi, I've been trying to recreate a SeppReferenceTree steps from thread:

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 …

1. I downloaded Exports/SILVA_138.1_SSURef_NR99_tax_silva_trunc.fasta and Exports/taxonomy/tax_slv_ssu_138.1.tre.gz from last SILVA release.
2. Then I run nw_topology -bI to prepare the tree.

I am intrested in creating SeppReferenceDatabase for V4 region specifically.

For the moment I am particularly puzzled with masking step described here.

• should I first filter reference sequences from SILVA to V4 region or do this masking step?
• how should I choose the masking length properly?
• should I take anything else into account to make the database reusable for community?

@dethlefs @hugh @Stefan your experience would be invaluable to accomplish this task.

Cheers!

[lizgehret]

Hi @crusher083, welcome back to the forum!

Our Data Resources linked from the user docs are going to be your best bet within QIIME 2 - if those don't address your questions, I'd recommend posing your questions in GitHub - smirarab/sepp-refs. Hope this helps!

Cheers,
Liz