There is no “one-size-fits-all” or “single-button” analysis that currently exists for fungal NGS data analyses (and I doubt there ever will be). My best advice is try multiple methods and see how the results compare. You might be as pleasantly surprised as I have been at how often you get the “same” ecological answer. Regardless of what you find, in your write-ups, be honest about the shortcomings of NGS (i.e. it is a tool not a question), make sure to write a detailed methods section so others can easily build from your work, and please be a vocal contributor if you find better methods.