Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing

Zaka Wing-Sze Yuen, Akanksha Srivastava, Runa Daniel, Dennis McNevin, Cameron Jack () and Eduardo Eyras ()
Additional contact information
Zaka Wing-Sze Yuen: EMBL Australia Partner Laboratory Network, Australian National University
Akanksha Srivastava: EMBL Australia Partner Laboratory Network, Australian National University
Runa Daniel: Victoria Police Forensic Services Department
Dennis McNevin: University of Technology Sydney
Cameron Jack: Australian National University
Eduardo Eyras: EMBL Australia Partner Laboratory Network, Australian National University

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: Abstract DNA methylation plays a fundamental role in the control of gene expression and genome integrity. Although there are multiple tools that enable its detection from Nanopore sequencing, their accuracy remains largely unknown. Here, we present a systematic benchmarking of tools for the detection of CpG methylation from Nanopore sequencing using individual reads, control mixtures of methylated and unmethylated reads, and bisulfite sequencing. We found that tools have a tradeoff between false positives and false negatives and present a high dispersion with respect to the expected methylation frequency values. We described various strategies to improve the accuracy of these tools, including a consensus approach, METEORE ( https://github.com/comprna/METEORE ), based on the combination of the predictions from two or more tools that shows improved accuracy over individual tools. Snakemake pipelines are also provided for reproducibility and to enable the systematic application of our analyses to other datasets.

Date: 2021
References: Add references at CitEc
Citations: View citations in EconPapers (8)

Downloads: (external link)
https://www.nature.com/articles/s41467-021-23778-6 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23778-6

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-021-23778-6

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().