Whole genome bisulphite sequencing using the Illumina X system [Infinium MethylationEPIC]

While Illumina X technology has helped to reduce the cost of whole genome sequencing substantially, its application for bisulphite sequencing is not straightforward. We describe the optimization of a library preparation and sequencing approach that maximizes the yield and quality of sequencing, and how to eliminate a previously unrecognized artefact affecting several percent of bisulphite sequencing reads. NA12878 and IMR90 cell ines assayed with Illumina Infinium MethylationEPIC BeadChip for comparison against whole genome bisulphite sequencing using BS-tagging protocol