title: epiGBS: reference-free reduced representation bisulfite sequencing.
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.
authors: Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands.
authors: Thomas P
authors: TP
authors: van Gurp
authors: Department of Experimental Plant Ecology, Radboud University, Nijmegen, the Netherlands.
authors: Niels C A M
authors: NC
authors: Wagemaker
authors: Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands.
authors: Björn
authors: B
authors: Wouters
authors: Plant Ecology and Nature Conservation Group, Wageningen University, Wageningen, the Netherlands.
authors: Philippine
authors: P
authors: Vergeer
authors: Department of Experimental Plant Ecology, Radboud University, Nijmegen, the Netherlands.
authors: Joop N J
authors: JN
authors: Ouborg
authors: Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands.
authors: Koen J F
authors: KJ
authors: Verhoeven
mesh_terms: D019175:DNA Methylation; D044127:Epigenesis, Genetic; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013447:Sulfites / Q000737:chemistry
chemical_list: D013447:Sulfites; C009279:sodium bisulfite