epiGBS: reference-free reduced representation bisulfite sequencing: brief communication

Thomas P van Gurp, Niels CAM Wagemaker, Björn Wouters, Philippine Vergeer, Joop NJ Ouborg, Koen JF Verhoeven

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Abstract

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.

Original languageEnglish
Pages (from-to)322-324
JournalNature Methods
Volume13
Issue number4
DOIs
Publication statusPublished - 2016

Keywords

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    van Gurp, T. P., Wagemaker, N. CAM., Wouters, B., Vergeer, P., Ouborg, J. NJ., & Verhoeven, K. JF. (2016). epiGBS: reference-free reduced representation bisulfite sequencing: brief communication. Nature Methods, 13(4), 322-324. https://doi.org/10.1038/nmeth.3763