I need to simulate a few metagenomics samples and I was thinking to use BBMap's simulator, randomreads.sh, in "metagenome" mode.
The problem is that I need to simulate the effect of PCR amplification, and I thought of including identical duplicates but with different quality scores.
Does anyone have any suggestion on how to do this? Or knows if BBMap randomreads.sh already simulates PCR duplicates (and if yes, how do I modify their proportion)?
Thanks a lot!