Bubbles in the de Bruijn graph.

Abstract

<p>(A) Representation of a simple 11 nt sequence as a de Bruijn graph (top) and then with a SNP (bottom). Nodes represent <i>k</i>mers – sequences of <i>k</i> nucleotides – and edges join together kmers that overlap by <i>k</i>−1 nucleotides. A SNP causes a bifurcation in the graph and the new path joins up with the original path after <i>k</i> nodes. (B) de Bruijn graph representations of a single heterozygous SNP (top) and a SNP followed by a second SNP within <i>k</i> nt (bottom). (C) Our bubble classification system assigns a type according to the number of colours present on each path through the bubble. Thus a bubble corresponding to a heterozygous SNP from an organism in which the resistant variant contains 2 alleles and the susceptible contains 1 allele would produce a bubble with 2 colours on one path and 1 colour on a second path and would be classified as a type “2,1”. Similarly, a bubble corresponding to a heterozygous SNP from an organism in which both the resistant and susceptible variants contain 2 alleles would be classified as a type “2,1”. Finally, a less common example where 2 alleles are present in one variant and 3 in another would appear as a type “2,2,1”.</p