Thanks for your patience, @Danilo_Reis. It’s been busy-busy around here lately! I’m not an expert with ITS sequencing, but I’ll share some resources that may help, and maybe others will chime in with their expert opinions.
This depends on what your study goals and workflow look like. Poor quality data may mean you lose some statistical power, but depending on the study needs and your sequencing depth, that could still be OK. Big-picture, I’d suggest trying to work with the data you have to see what it can get you. Worst-case scenario, if you need to consider collecting additional samples or re-sequencing, you have a clearer picture of what your requirements are.
Attempting to join poor-quality reads with DADA2 will probably (and justifiably) drop many of your sequences. Check out the “Denoising” section of @Nicholas_Bokulich 's Fungal ITS analysis tutorial for advice on selecting a good denoising workflow for your data.0
If you have doubts about the work done by the sequencing company, you can always manually trim the raw data. Depending on your situation, (e.g. do you have access to the primer sequences) q2-cutadapt and q2-itsxpress can both be useful.
Let us know how it goes!