I have a quick question regarding DADA2. I was told that I should not be using Quiime2 to work on ITS data, because DADA2 filtering and trimming steps are based on bacterial databases and due to the variability in the ITS primers, this could change my data. I wanted to see if this was still the case and if you reccomend I use QUIIME1 instead.
That is totally false. dada2 does not use any databases — it trains an error model based on the error rates observed in the run itself. I believe the original dada2 paper was benchmarked on bacterial community data, but there is no evidence to suggest that ITS data are going to exhibit different error rates on a sequencing run, requiring different methods.
dada2 is pretty widely used for ITS at this point. In addition to the tutorials that @Mehrbod_Estaki highlighted, you may also want to check out the q2-itsxpress tutorial, which uses q2-itsxpress to trim ITS reads prior to denoising with dada2: