processing paired reads

[pedres]

Hi,
I was searching here and in the manual but I am not sure how to proceed. I want to classify a sample with paired reads and I understand that I have to pass --paired flag. However, in the "Metagenome analysis using the Kraken software suite" for the microbiome protocol the kraken2 command has not the --paired flag as it appears in the pathogen protocol. When looking at the code on https://github.com/martin-steinegger/kraken-protocol none of the kraken2 commands have the --paired flags.
So, what would be the correct approach to process a set of paired reads?
Thank you very much for your help

Manuel