De Bruijn Graphs - III

In earlier commentaries, we introduced the concept of de Bruijn graphs and showed how they were used for de novo assembly of short read sequences. If you read the posts, you likely left with an impression that de Bruijn graphs were useful weapons to be included in all bioinformaticians’ arsenals. However, none of the posts clearly explained, why they became the primary weapons applied by all popular short read assemblers. Let us do that at the outset here.

We will borrow the following figure from our previous post. It shows de Bruijn graph of a genome, and few short reads aligned to the genome and the de Bruijn graph. Like before, we will restrict our discussions to the perfect world with no countries, no religion, no greed or hunger and, most importantly, no sequencing error.

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