De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer

Fixing bubbles. This illustration shows a bubble caused by a polymorphism. This example is one of the many that can be found in the overlap graph constructed from the Staphylococcus aureus strain MW2 reads data set. (A) The 24 reads implicated in the bubble are shown. r₁ and r₂₄ are the ends of the bubble, which is 35 × 2 + 1 bp in length. Reads showing the polymorphism are r₁₁ to r₁₅. None of these reads have exact occurrence in the published genome of S. aureus strain MW2 sequence. (B) The corresponding transitively reduced overlap graph is shown. By considering the read redundancy, the total number of reads in the low and highly covered side is five and 27, respectively. Fixing of bubbles consists in removing nodes forming the less covered side of the bubble.