Fig. 2

Examples to show how BioNanoAnalyst assesses the quality of NGS genome assembly. In the examples we assume that there are 6 selected enzyme cut sites (e.g. Nt.BspQI) on the NGS reference. Five different mapping cases are given to assist the understanding of the scoring in BioNanoAnalyst. a shows a good match between NGS reference and BioNano map, and BioNanoAnalyst gives score 4 to each restriction site on the NGS reference. b shows a conflict in the number of mapped restriction site between matched adjacent restriction sites. In this case, BioNanoAnanlyst assigns 3 to site 1–3. c shows a physical distance matching conflict (diff falls outside one of the boundaries) between mapped NGS reference and BioNano map. In this case, BioNano scores site 1 and 2 with score 2. d shows a physical distance matching conflicts and number of restriction site matching conflict between NGS reference and BioNano map. In this case, score 1 is given to site 1–3. e shows a case that there is no BioNano map mapping to some sites on the NGS reference, such as site 1 and 2. In this case BioNanoAnalyst gives score 0 to site 1 and 2