Comparison of Oxford nanopore and Illumina Epic sequence data for methylation analysis

Long read data from Oxford Nanopore offers the dual benefit of very long reads while also retaining methylation information. Methylation calls were derived from Nanopore signal using the software Nanopolish and compared with targeted Illumina Epic methylation data from the same cell line. Public whole genome Illumina (WGBS) data was also integrated into the comparison. Results indicate broad agreement between the techniques, with Nanopore and WGBS being the most comparable techniques, even at a relatively low nanopore coverage. Nanopore data also displays increased mappability in repetitive region due to sequence length. As nanopore data becomes more widely used, we envisage the complementary methylation byproduct to be have a significant impact in cancer genetics.