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. 2024 Mar 11;25:69. doi: 10.1186/s13059-024-03207-9

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 1 — Nanopore sequencing and oxBS performance in the same DNA samples. The consistency in 5-mCpG rates measured by nanopore sequencing and oxBS in DNA samples isolated from the same 132 individuals was estimated by the following: A The overall measurement of 5-mCpG rates in each of the 132 DNA samples measured by ONT (red) and oxBS (green), Y-axis is limited to (0.7,0.8). The center line (solid black) shown in each box represents the median; the box limits represent the upper and lower quartiles; the whiskers represent 1.5 × interquartile range. B The Pearson r correlation coefficient, y-axis, and C mean of the absolute differences in 5-mCpG rates of each CpG, y-axis, with respect to nanopore sequencing coverage in each sample on the x-axis. Panels D, E, and F analyze sites that have > 25 × coverage in oxBS. D CpG coverage underlying the 5-mCpG rates, i.e., the number of sequences that were used to compute the 5-mCpG rate for a given CpG, in nanopore sequenced samples, x-axis, influences the consistency (Pearson r), y-axis, with 5-mCpG rates measured with high coverage by oxBS. The y-axis is limited to (0.5, 1) E CpG rates in nanopore (y-axis) and oxBS (x-axis, binned). The mean is represented with red (ONT) and green (oxBS). F Number (y-axis, unit = million CpGs) of correctly classified (blue) by nanopore sequencing in a sample-to-sample comparison. Incorrectly classified CpGs are colored according to the absolute difference in 5-mCpG rates (color legend)