insert size for PE versus MP reads

[000generic]

Hi!

I was wondering what you recommend for structuring sets of forward and reverse reads to provide to MAC when read length and insert size are variable.

Our PE insert size is ~200 bp but MP insert sizes vary from 500-2000 bp. Should all of these reads be combined into single forward and reverse sets? if so, what should I provide for insert size and read length? Or should I create sets of forward and reverse reads based on read length and insert size? If so, how should I structure the command line to run MAC?

I also was wondering, will MAC work for animal genomes? Or is designed more for bacteria and viruses and/or other smaller genomes?

Thank you for your help!