The effect of sampling depth. Here we plot the residual deviance of the linear model applied to the error gradient of a 200 bp fragment for various step sizes. Each curve corresponds to a particular step size for a fixed sequence length. Notably, the effect of step size is independent of sampling depth, and further a sampling depth of 20 gives a good model for the reduction in error over sequence length for sequences in the order of magnitude considered in the benchmarks. Intuitively, larger sequence lengths will require greater sampling depths.
Saeed and Halgamuge BMC Genomics 2009 10(Suppl 3):S10 doi:10.1186/1471-2164-10-S3-S10