Introduction

We describe epiGBS, a reduced representation bisulfite sequencing method for cost-effective exploration and comparative analysis of DNA methylation and genetic variation in hundreds of samples de novo. This method uses genotyping by sequencing of bisulfite-converted DNA followed by reliable de novo reference construction, mapping, variant calling, and distinction of single-nucleotide polymorphisms (SNPs) versus methylation variation (software is available at https://github.com/thomasvangurp/epiGBS). The output can be loaded directly into a genome browser for visualization and into RnBeads for analysis of differential methylation.

Publications

  1. epiGBS: reference-free reduced representation bisulfite sequencing.
    Cite this
    van Gurp TP, Wagemaker NC, Wouters B, Vergeer P, Ouborg JN, Verhoeven KJ, 2016-04-01 - Nature methods

Credits

  1. Thomas P van Gurp
    Developer

    Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)

  2. Niels C A M Wagemaker
    Developer

    Department of Experimental Plant Ecology, Radboud University

  3. Björn Wouters
    Developer

    Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)

  4. Philippine Vergeer
    Developer

    Plant Ecology and Nature Conservation Group, Wageningen University

  5. Joop N J Ouborg
    Developer

    Department of Experimental Plant Ecology, Radboud University

  6. Koen J F Verhoeven
    Investigator

    Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)

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Summary
AccessionBT000283
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByKoen J F Verhoeven