Table 1

Statistics of the de Bruijn graphs and optical maps used in our simulations
Min Median Mean Max
Nodes 1 35 63.63 1,023
Edges 3 110 324.4 14,251
N50 Size (kbp) 14 212.1 419.2 3,587
Genome Length (Mbp) 0.34 2.91 3.2 9.14
Restriction Sites 6 334 491.7 9,668

The de Bruijn graphs for 369 bacterial genomes were generated with k-mer size 100 from the known sequences from [34] (without errors and without bubble collapsing), and the N50 size was computed for each genome, treating each edge in the de Bruijn graph as a separate contig. The row “Restriction Sites” refers to the number of cuts within the genome when using the restriction enzyme BamHI.

Lin et al.

Lin et al. BMC Bioinformatics 2012 13:189   doi:10.1186/1471-2105-13-189

Open Data