We describe epiGBSBS, a reduced representation bisulfite sequencing method for cost-effective exploration and comparative analysis of DNADNADNA methylation and genetic variation in hundreds of samples de novo. This method uses genotyping by sequencing of bisulfite-converted DNADNADNA followed by reliable de novo reference construction, mapping, variant calling, and distinction of single-nucleotide polymorphisms (SNSNPs) 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.
|Journal||Nature Methods : techniques for life scientists and chemists|
|Publication status||Published - 2016|
van Gurp, T., Wagemaker, C. A. M., Wouters, B., Vergeer, P., Ouborg, N. J., & Verhoeven, K. J. F. (2016). epiGBSBS: reference-free reduced representation bisulfite sequencing. Nature Methods : techniques for life scientists and chemists, 13, 322-324. https://doi.org/10.1038/nmeth.3763