Introduction

In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanopore Technologies MinION sequencer. By using synthetically methylated DNA, we were able to train a hidden Markov model to distinguish 5-mC from unmethylated cytosine. We applied our method to sequence the methylome of human DNA, without requiring special steps for library preparation.

Publications

  1. Detecting DNA cytosine methylation using nanopore sequencing.
    Cite this
    Simpson JT, Workman RE, Zuzarte PC, David M, Dursi LJ, Timp W, 2017-04-01 - Nature methods

Credits

  1. Jared T Simpson
    Developer

    Department of Computer Science, University of Toronto, Canada

  2. Rachael E Workman
    Developer

    Department of Biomedical Engineering, Johns Hopkins University, United States of America

  3. P C Zuzarte
    Developer

    Ontario Institute for Cancer Research, Toronto, Canada

  4. Matei David
    Developer

    Ontario Institute for Cancer Research, Toronto, Canada

  5. L J Dursi
    Developer

    Ontario Institute for Cancer Research, Toronto, Canada

  6. Winston Timp
    Investigator

    Department of Biomedical Engineering, Johns Hopkins University, United States of America

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Summary
AccessionBT003525
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByWinston Timp