Hi all, as a bioinformatics project, I'm taking metagenome project reads from ebi database, but I am wondering if there any suggestion for comparative metgenomic analysis pipeline/programs that could explore functional differences in choosen two microbiome samples. Mostly prokaryotic.

I.e., comparing the metagenome from two clusters samples determined from pca analysis

Or even other websites or resources I should look into

Thanks in advance!