Impact of restriction enzyme choice on assembly quality. The choice of restriction enzymes can impact the correctness of the assembly. Each point represents the sequence correctness of an assembly of Y. pestis KIM when given a de Bruijn graph of k-mer size 100 and an optical map of low, medium, or high error rate. The vertical line in the picture indicates the number of restriction sites for the enzyme PvuII used to construct the experimental optical map of this genome, and the colored circles represent the correctness that can be achieved under the three error rates for the PvuII enzyme. The red, blue, and green filled squares to the right of the vertical line, indicate an improvement of between 7.7% and 30.1% in the final sequence correctness that can be achieved when choosing a better restriction enzyme in the high, medium, and low error settings, respectively.
Lin et al. BMC Bioinformatics 2012 13:189 doi:10.1186/1471-2105-13-189