Update `SeppReferenceTree` to SILVA 138.1

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

  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.


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Hi @crusher083, welcome back to the :qiime2: 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!


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