FIG. 1.

Mate pairs and the de Bruijn graph. (a) A mate pair is a pair of reads with a distance of d between their start positions. (b) A circular genome S and two mate pairs, with d = 4 and d = 5. (c, d) The de Bruijn graph construction for k = 2. (c) The outside circle shows a separate black edge for each 3-mer (equivalently, each element of the 3-spectrum). The dotted red lines indicate vertices that will be glued. The inner circle shows the result of applying some of the glues. Note that this is an intermediate step of the construction in which we only show the gluings of vertices arising from the same position of S. (d) The final de Bruijn graph, resulting from all the glues.