IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-021-23778-6.html
   My bibliography  Save this article

Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing

Author

Listed:
  • Zaka Wing-Sze Yuen

    (EMBL Australia Partner Laboratory Network, Australian National University
    Australian National University)

  • Akanksha Srivastava

    (EMBL Australia Partner Laboratory Network, Australian National University
    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
    Australian National University
    Catalan Institution for Research and Advanced Studies (ICREA)
    Hospital del Mar Medical Research Institute (IMIM))

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.

Suggested Citation

  • Zaka Wing-Sze Yuen & Akanksha Srivastava & Runa Daniel & Dennis McNevin & Cameron Jack & Eduardo Eyras, 2021. "Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23778-6
    DOI: 10.1038/s41467-021-23778-6
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-021-23778-6
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-021-23778-6?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Zhen-Dong Zhong & Ying-Yuan Xie & Hong-Xuan Chen & Ye-Lin Lan & Xue-Hong Liu & Jing-Yun Ji & Fu Wu & Lingmei Jin & Jiekai Chen & Daniel W. Mak & Zhang Zhang & Guan-Zheng Luo, 2023. "Systematic comparison of tools used for m6A mapping from nanopore direct RNA sequencing," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Peng Ni & Neng Huang & Fan Nie & Jun Zhang & Zhi Zhang & Bo Wu & Lu Bai & Wende Liu & Chuan-Le Xiao & Feng Luo & Jianxin Wang, 2021. "Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    3. Peng Ni & Fan Nie & Zeyu Zhong & Jinrui Xu & Neng Huang & Jun Zhang & Haochen Zhao & You Zou & Yuanfeng Huang & Jinchen Li & Chuan-Le Xiao & Feng Luo & Jianxin Wang, 2023. "DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Xue Yue & Zhiyuan Xie & Moran Li & Kai Wang & Xiaojing Li & Xiaoqing Zhang & Jian Yan & Yimeng Yin, 2022. "Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23778-6. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.