Fig. 4

A comparison between the quality of the scores of the alignments found by the various methods on the plum data. All alignments were realigned using the dynamic programming method of Valouev et al. [12] in order to acquire a score for each alignment. Hence, the method finds the optimal alignment using a function balancing size agreement and cut site agreement known as a S-score. The following alignments were considered: a those obtained from aligning random pairs of Rmaps; b those obtained from the method of Valouev et al. [12]; c those obtained from Kohdista; d those obtained from MalignerDP; e those obtained from OMBlast; and lastly, f those obtained from BioNano’s commercial RefAligner