Processing ITS2 amplicons from pollen

I am trying to process ITS2 amplicons from pollen. The authors of the publication where we took the methodology from used MEGAN developed by folks from the University of Tubingen in Denmark. I went to their website and it turns out MEGA6 is a microbiome analysis tool. Before I learn a new tool I wanted to make sure Qiime2 wouldn’t do the same thing?
Thank you
Fernando

Sure! QIIME 2 could be used for this as long as your format your data appropriately. Any of the classifiers in q2-feature-classifier would be appropriate, though classify-consensus-vsearch is probably the most similar to MEGAN (which I believe also uses LCA for consensus assignment)

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