JaBbA builds a genome graph based on junctions and read depth from whole genome sequencing, inferring optimal copy numbers for both vertices (DNA segments) and edges (bonds between segments). It can be used for discovering various patterns of structural variations. If you use JaBbA in your work...
Weinfeld et al., “Selective hydrolysis by exo- and endonucleases of phosphodiester bonds adjacent to an apurinic site”. Nucleic Acids Research, vol. 17, No. 10: 3735-3744 (1989). Weissenbach et al. “A Second generation linkage map of the human genome”. Nature, vol. 359, pp. 794...
adding all copies a segment has, the simple rule that cannot be broken is there must be same number of copies of up/downstream neighbors. If we treat segments as vertices and the 3'-5' phosphodiester bond between segments as edges, we get thejunction balance constraintsthat couple them ...