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bioRxiv · 10.1101/2021.05.05.442849

DNA methylation calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation

Liu, Y.·Rosikiewicz, W.·Pan, Z.·Jillette, N.·Taghbalout, A.·Foox, J.·Mason, C.·Carroll, M.·Cheng, A.·Li, S.
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Abstract

BackgroundNanopore long-read sequencing technology greatly expands the capacity of long-range single-molecule DNA-modification detection. A growing number of analytical tools have been actively developed to detect DNA methylation from Nanopore sequencing reads. Here, we examine the performance of different methylation calling tools to provide a systematic evaluation to guide practitioners for human epigenome-wide research. ResultsWe compare five analytic frameworks for detecting DNA modification from Nanopore long-read sequencing data. We evaluate the association between genomic context, CpG methylation-detection accuracy, CpG sites coverage, and running time using Nanopore sequencing data from natural human DNA. Furthermore, we provide an online DNA methylation database (https://nanome.jax.org) with which to display genomic regions that exhibit differences in DNA-modification detection power among different methylation calling algorithms for nanopore sequencing data. ConclusionsOur study is the first benchmark of computational methods for mammalian whole genome DNA-modification detection in Nanopore sequencing. We provide a broad foundation for cross-platform standardization, and an evaluation of analytical tools designed for genome-scale modified-base detection using Nanopore sequencing.

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Liu, Y., Rosikiewicz, W., Pan, Z., Jillette, N., Taghbalout, A., Foox, J., Mason, C., Carroll, M., Cheng, A., Li, S.. 2021-05-06. DNA methylation calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation. https://doi.org/10.1101/2021.05.05.442849

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