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

Removing transitive edges. A read r₁ with 13 other reads (r₂ . . . r₁₄) that overlap on its right end side are shown in the form of a multiple alignment. The overlaps that do not correspond to transitive edges are indicated with a black dot. The transitive edges removal procedure consists in discarding the overlaps that are already overlapped by another read involved in a larger overlap with r₁. For example, the reads r₄, r₆, r₇, r₁₀, r₁₁, r₁₃, and r₁₄ are overlapped by r₂; they are therefore removed from the set of overlapping reads of r₁. Same principle is applied to the reads r₃, r₅, and r₈. This example is issued from a real data set of reads of 26 bases.