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Next generation sequencing (NGS) is revolutionizing all fields of biological research but it fails to extract the full range of information associated with genetic material. Complementary genomic technologies that analyze individual, unamplified genomic DNA are filling the gaps in the capabilities of NGS. Using such technologies we gain access to the structural variation and long range patterns of genetic and epigenetic information. Recent results from our lab demonstrate our ability to detect and map the epigenetic marks 5-methylacytosine and 5-hydroxymethylcytosine as well as various forms of DNA damage on individual genomic DNA molecules. This new technology allows genetic and epigenetic variation calling on the single cell level without the need to process single cells.