I have a high number of bacterial cultures I am growing, extracting the DNA from, and sequencing as short reads. Due to the format I'm using (96-well plates), cross-sample contamination is a big concern. It's been suggested I analyze the heterozygosity of the assembled genome (ideally: none) as a proxy measure for cross-contamination.
Does anyone have experience in doing this and can recommend tools for this?
Alternately, does anyone have other suggestions for tackling this problem and detecting cross-contamination specifically at the short read data stage?