Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing [Beadchip]

We systematically evaluated alternate strategies for WGBS studies, taking into account opportunites around library preparation methods, sequencing platforms and analysis pipeline optimization. We also assessed the performance and precision of the WGBS method relative to the methylation arrays, in an effort to provide data-driven recommendations for future WGBS studies, in particularly with respect to minimum coverage. Bisulfite-converted DNA for 8 human samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip and Illumina Infinium HumanMethylation850 BeadChip. Whole genome bisulphite sequencing libraries for 8 human samples were prepared by different methods with low DNA input requirement and sequenced by Illumina NovaSeq and HiSeq X10 platforms.