A Drawback of de Bruijn Graph Approach

In our first commentary on de Bruijn graphs, we explained how de Bruijn graph can be constructed for any genome.

In the second commentary, we argued that a de Bruijn graph created from millions of short reads is identical to the de Bruijn graph of the underlying genome, if coverage is perfect. So, the assembly problem reduces to figuring out the genome from its de Bruijn graph, i.e. the inverse problem of graph creation.

At this point, you may be wondering why de Bruijn graphs were not widely used in the prehistoric era of sequencing (Sanger sequencing era) given that they are the greatest things invented since sliced bread. The answer is simple. De Bruijn graphs do not preserve positional information.

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