Picking OTU's with samples generated by different primers

[Náthali Machado]

Hello, I am trying to contact you to see if you could help me...
I need to analyse differents data to do biodiversity comparison, and I have data generated using bacteria general primers and sample using cianobacterial primers, but they overlap in 200 bp. I would know how can paired all the fowards and reverses, align all togheter, trim just this region and then pick OTU's?

Thank you so much!