I’m getting familiar with the q2-fragment-insertion plugin, now available in qiime 2019.1
I was able to follow the tutorial and generate the tree (note: this plugin does not seem to work in WSL, I had to use Virtualbox in my windows system, in which it ran with no problems).
After that, I exported the SEPP tree to obtain the file in *.nwk format. Then, I uploaded the tree to ITOL with no problems. When I try to add the taxonomy file, as the tips in the uploaded tree no longer contain the ASV hast tags (it has some numbers, though), I receive this message: “Couldn’t find ID 01e51045bda814ec780fcfb7613ccc1b in the tree”. With the original tree (before using the fragment insertion plugin), I didn’t have any issues.
Interestingly, I can merge the new tree with the BIOM file (created from my data) in the phyloseq package with no problems.
I really appreciate any advice on this.