Fig. 6

Outline of minimap2’s chaining. a shows for an anchor (in green) the selected region (in white, G is the gap threshold) to find available anchors to continue chaining (in blue). b and c give respectively the dynamic programming functions for regular and large gaps size. Anchors are shown as segments ending with green or blue dots with the same color code as in a. Besides, for the large gap size (c), to improve the complexity, the anchors do not overlap (available anchors are not in the red zone). \(d_{ji}\) represents the smallest “distance” between the two anchors (but is not really a distance by definition), w is the minimizer window size, \(g_{ji}\) is the gap length, and the \(\gamma\) functions are the concave gap functions