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bioRxiv · 10.1101/2021.04.24.441281

A comparative analysis of computational tools for the prediction of epigenetic DNA methylation from long-read sequencing data

Pai, S. S.·Mathew, A. R.·Anindya, R.
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Abstract

Recent development of Oxford Nanopore long-read sequencing has opened new avenues of identifying epigenetic DNA methylation. Among the different epigenetic DNA methylations, N6-methyladenosine is the most prevalent DNA modification in prokaryotes and 5-methylcytosine is common in higher eukaryotes. Here we investigated if N6-methyladenosine and 5-methylcytosine modifications could be predicted from the nanopore sequencing data. Using publicly available genome sequencing data of Saccharomyces cerevisiae, we compared the open-access computational tools, including Tombo, mCaller, Nanopolish and DeepSignal for predicting 6mA and 5mC. Our results suggest that Tombo and mCaller can predict DNA N6-methyladenosine modifications at a specific location, whereas, Tombo dampened fraction, Nanopolish methylation likelihood and DeepSignal methylation probability have comparable efficiency for 5-methylcytosine prediction from Oxford Nanopore sequencing data.

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Pai, S. S., Mathew, A. R., Anindya, R.. 2021-04-26. A comparative analysis of computational tools for the prediction of epigenetic DNA methylation from long-read sequencing data. https://doi.org/10.1101/2021.04.24.441281

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