Hi @MiriamGorostidi
Just to qiime in on coupe of point, @timanix please add anything you feel is missing!
On ITSxpress, please see:
There is a q2-itsxpress plug in at:
https://library.qiime2.org/plugins/q2-itsxpress/8/
Pleas note, you may need an older version of qiime2 to work with this, I am not sure.
There are few threads already on this.
A possible full tutorial is:
It basically extract the ITS region removing any extra bases around, which may be useful to clean up the sequences for the taxonomy step.
On the classifier, yes I woul dgive a tray using blast classifier on your current rep-seq. My understanding of vsearch is that still uses a global alignment, in which query and target need to match from head-to-tail, while blast will focus on matching possible sub-sequences of your rep set on the sequences in the database.
Good luck and let us know any progress.
Cheers
Luca