Hi @Abdullah1,
Welcome aboard!
To use DADA2 for paired-end reads check out the documentation for dada2 denoise-paired
here, you can also get these help files in any qiime2 command by adding the --help
tag after whatever action you’re interest in. That being said, since you are using ITS sequences, have a look through this new tutorial specific for ITS amplicons as it covers some important and ITS-specific points that should be considered.
Hope that helps!