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Table 1 Statistics of the de Bruijn graphs and optical maps used in our simulations

From: AGORA: Assembly Guided by Optical Restriction Alignment

 

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

  1. 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.
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BMC Bioinformatics

ISSN: 1471-2105

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