Strategies for

-mer choice under the different models. Error is measured as the sum of squared differences between true and estimated matrices. The plot presents, for different error thresholds, the number of runs out of which yielded a precision at least as small as the threshold. Using the original model, we extracted from each 100 bp read either the first -mer, 9 sparely dispersed -mer along it, 24 non-overlapping -mers or 96 overlapping -mers. Extracting multiple -mers can be seen to increase precision considerably. Shifting to the refined model yields an even better precision; since this model is more sensitive to dependencies between -mers, extracting only the fewer dispersed -mers is preferable over extracting all non-overlapping -mers.