Modification of DNA resulting in 5-methylcytosine (5 mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. Although recent advances in next generation sequencing technology allow researchers to map epigenetic modifications across the genome, such experiments are often time-consuming and cost prohibitive. Here we present a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially available semiconductor based technology (DNA immunoprecipitation semiconductor sequencing; " DIP-SC-seq ") on the Ion Proton sequencer. Focussing on the 5hmC mark we demonstrate, by directly comparing with alternative sequencing strategies, that this platform can successfully generate genome wide 5hmC patterns from as little as 500 ng of genomic DNA in less than 4 days. Such a method can therefore facilitate the rapid generation of multiple genome wide epigenetic datasets. The advent of next-generation sequencing (NGS) technology has resulted in a tremendous acceleration in the rates at which large sets of transcriptional, genetic and epigenetic data can be generated and analysed; impacting on a wide range of scientific disciplines 1,2. Today's sequencing based experiments typically generate more data than alternative methods such as microarray based assays; allowing the researcher to carry out high resolution analyses such as quantification of both transcriptional activity (RNA sequencing: RNAseq) and epigenetic modification patterns (DNA modification sequencing; " DIP-seq " and chromatin immunoprecipitation sequencing; " ChIP-seq " 3–5