Figure 3

Schematic representation of the OC chaining procedure, depicting the cases OC can deal with and the ones it cannot. Overlap Chaining (OC) fragment chaining procedure illustrated schematically with a dotplot on an example composed of ten fragments (i.e., segments around the diagonal of the dotplot and their projections on the two axis), among which seven fragments were taken in the chain (i.e., dark blue, light blue, dotted blue and violet ones). The main chaining cases are summarized in the figure in four ellipses, namely: (a) a simple case represented by the two dark blue, collinear, non-overlapping fragments (classical chaining case) plus a local inversion (represented by the violet fragment), which becomes collinear after inversion with OC, and thus it is taken in the chain; (b) a translocation depicted by two red fragments: due to the collinearity constraints, only one fragment among the two can be taken in the chain, thus the algorithm prefers the “strongest” one, i.e. the dotted blue; (c) three overlapping fragments, among which only two are accepted in the chain (the light blue ones) as they overlap on less than 10% of their respective length; the red fragment is discarded as its overlaps are above the accepted threshold; (d) a double inversion represented by two inversed fragments from which only one can be taken in the chain (the violet one); by inversing the two fragments, OC generates a translocation-like situation, and thus it can only consider one fragment among the two.