Fig. 2

The figure compares Dynamic Programming (gray), MEMs (black), MA (orange), Minimap2 (red), NGMLR (green), and GraphAligner (blue) regarding the rediscovery of several types of SV. The human genome GRCh38.p12 is used as the reference genome. Subfigure A visualizes the analyzed genomic rearrangements using diagrammatic dot-plots. Blue lines indicate matches on the same strand, while orange lines represent matches on opposite strands. A description of diagrammatic dot-plots can be found in Additional file 2. Subfigure B displays the rediscovery rate as a function of the SV size (see subfigure A) for the various kinds of SV in A. Each diagram shows two curves. Here, each point of a curve represents an average measurement for 1000 query sequences. The lighter-colored areas show recall rates for idealized error-free queries, while the darker areas report rates for simulated PacBio CCS reads. The diagrams for Dynamic Programming show rediscovery rates for banded global Dynamic Programming with two-piece affine gap costs. Here, the global Dynamic Programming is merely applied to the reference section that a query originates from