Algorithm for estimation of inter-scaffold gap lengths. (A) Scatter plot, with dots showing the physical position on the chromosome versus the genetic position. Vertical lines mark the boundaries of the component scaffolds. Cubic spline is used to generate interpolation of genetic distance along the chromosome. (B) Recombination rates, measured in centiMorgans per Mb (cM/Mb), are estimated by taking the derivative of the cubic spline. Circles represent the locations of the inter-scaffolds gaps. (C) An example of the size estimation of one gap between two adjacent scaffolds.