Fragment-insertion plugin - question about SEPP reference databases

Hi Everyone,

Happy new year for everyone!
Just some clarifications about the SEPP reference databases.
If I use a trained taxonomic classifier (based on SILVA) for my taxonomic analyses, can i use the Greengenes 13_8 SEPP reference database? I’m asking because this approach is much less computational intense to obtain the insertion-tree.qza.
If my trained taxonomic classifier is based on SILVA 132, would there be any issues using the Silva 128 SEPP reference database?

Thanks in advance,

Hi @fstudart,
If I understand your question right you want to know whether you can use a classifier trained on the SILVA database for your taxonomy assignments and use Greengenes for SEPP fragment-insertion tree building. The answer is technically yes, since these are 2 different entities and are not linked together in Qiime2. When information about a feature is needed (taxonomy or phylogeny in this case) Qiime2 is reaching into 2 separate objects so they are not interfering with each other. Is it recommended? :man_shrugging:, ideally you would stick consistent with 1 database but I don’t have a good reason as why I feel that way.

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.