Great idea!
When thinking about contamination removal, I guess I want to start with known sources first, because our understanding of their mechanism gives us a starting point when we try to reverse their effect. So I'm nominating crosstalk as our first target for contaminate removal.
Of course Robert Edgar already has a method for this: software & paper PDF
I can contribute a large data set of positive controls, of a verity of microbes, grown in monoculture, over a period of years. This is an ideal data set for addressing how many external reads get added into a clonal sample from Illumina crosstalk.
Colin
I like this idea! Now how could we build a benchmark that demonstrates that our common sense is doing a good job finding and removing contaminates. Because you know reviewer 3 had no common sense at all 