Silva database in sepp format for phylogeny tree

[RMallick (River Mallick)]

Hi, I am using the silva 138 ssu database to analyze my 18S samples, and I am trying to create a phylogeny tree. So far, this database has worked fine for me, but I am running into an issue with the format? Here is the code and error I am running into. I recognize that I need to have the database in the sepp format, but I'm unsure how to do that?

qiime fragment-insertion sepp --i-representative-sequences ./dada2_rep_set.qza --i-reference-database silva_138.qza --o-tree ./tree.qza --o-placements ./tree_placements.qza --p-threads 1

Error:
Invalid value for '--i-reference-database': Expected an artifact of at

least type SeppReferenceDatabase. An artifact of type TaxonomicClassifier

was provided.

[Keegan-Evans]

@RMallick,

You should be able to just use SILVA 138 to classify, then if you do want to use SEPP, you can get the SILVA 128 SEPP reference database from the bottom of the data-resources page.

I also reached out to another moderator who made some resource suggestions and additional steps if you want to build your own SEPP database:

• Trouble generating SeppReferenceDatabase qza
• Build a SILVA tree using FastTree
• Then simply place the various files into a directory like so, and import using the SeppReferenceDatabase type, with the following files:
  • aligned-dna-sequences.fasta
  • tree.nwk
  • raxml-info.txt

Neither of us have ever actually needed to run this workflow, so let us know if you run into any difficulties, but that should get you headed in the right direction!