Automating consensus sequence generation...?

[SDK]

I have a rather straightforward problem. I'm doing a pop. gen. study which has ~1200 individuals. Using our Miseq, I've generated short (~150b) fragments for these individuals at 5 loci (one direction, not paired end). I'd like to know the best way to generate consensus sequences for each individual at each loci (4800 samples). There must be an automated way or at least a superior program?

Thanks