I’m trying to follow this https://library.qiime2.org/plugins/q2-fragment-insertion/16/ tutorial and I’m currently stuck on this step
qiime fragment-insertion classify-otus-experimental
My problem is that the link to the taxonomy_gg99.qza is broken, nor is this reference taxonomy explained well. May I use the reference taxonomy I trained for my primers? Is this reference taxonomy 16S (515F/806R) specific? I’m guessing so since the previous parts of the workflow referenced the moving pictures tutorial, but it is not clear.
Finally, it appears that the file phylogeny.qza is not a standard .nwk tree file which I will need for further analysis (specifically calculating MNTD using the picante package). Is there was way to create this?