FIG. 4.

Example of the standard and paired de Bruijn graphs: The reads are the (5,12)-spectrum generated from the cyclic sequence ATCGGGATGACTATGTCGCTCCTAATCGGGAAGACTATGCCGCTCCTT. (a) The de Bruijn graph with edges constructed from the set of 5-mers in the (5,12) spectrum. Each node is a rectangle labeled by a 4-mer with the node ID shown as a large red number on the left of the node. The mate pair information is also presented in the graph: for each node, the node IDs of its corresponding right 4-mers are shown as small numbers on the right of the rectangle. For instance, the right 4-mers (blue dotted lines) of CGGG (node 3) are GTCG (node 21) and GCCG (node 22) and we write 21 and 22 on the right side of node 3. Note that there is not a single mate pair with a unique path between the mates, making mate pair transformations impossible. (b) The paired de Bruijn graph from the (5,12) spectrum is a cycle, representing a single contig. In this example, the paired approach allows for longer contigs than would mate pair transformations (though there are also examples when the opposite is true).