Creating contaminated synthetic reads

Question

[matt81rd]

Hi all,

I know there are a few programs out there for detecting and removing contamination from reads, but i am looking to actually create contaminated reads. I have just finished some work creating synthetic reads with the ability to have known variance in that genome using NEAT (https://github.com/ncsa/NEAT), and now i need to create contaminated (species mixture) synthetic reads to test a tool that my department has created. Shot in the dark but does anyone know of a already existing tool that does this? I don't want to have to reinvent the wheel if its already been done previously.

Many thanks!

[Mensur Dlakic]

Why not create synthetic reads for the contamination species using the same procedure and simply add them to your original dataset?