I need advice on SEPP. Is it possible to import DADA2-generated (R) rep.seqs to QIIME2 and make fragment-insertion sepp tree?
I found this information useful, but I am not sure if using Silva 128 SEPP Reference Database would be problematic, given that I have used Silva 138 for the taxonomy.
In case it is OK to use Silva 128, would the following workflow be correct?
qiime tools import \
--input-path repseqs.fasta \
--output-path repseqs.qza \
--type "FeatureData[Sequence]
Followed by:
qiime fragment-insertion sepp \
--i-representative-sequences ARTIFACT FeatureData[Sequence] \
--i-reference-database ARTIFACT SeppReferenceDatabase \
--o-tree ARTIFACT Phylogeny[Rooted] \
--o-placements ARTIFACT Placements
Thank you,