Next Generation Sequencing (NGS) instruments have enabled scientists to decode the basic sequence of DNA on a massive scale and to unlock major discoveries in areas as diverse as human health, evolution, and ecology. However, being able to read the four bases of DNA is far from sufficient to be able to understand all of the genetic world around us. In human genetics, for example, even though many tens of thousands of human genomes have now been sequenced, a large fraction of human genetic variation cannot be well correlated to common human diseases (e.g. heart disease, cancer, obesity, etc.). In recent years, new levels of genetic complexity have been uncovered with the discovery of different types of molecular switches that control the activity of the genes encoded by DNA. Two types of molecular switches are extremely important in modulating genetic activity: (1) variations in the different forms of RNA, and (2) the base-modifications – a set of chemical groups can be added to the bases of both DNA and RNA. It is now clear that full genome analysis requires the sequencing of not only DNA, but also RNA and the base modifications on these molecules. Current NGS instruments are very good for reading DNA sequence, but are severely limited in their capacity to analyse RNA and base-modifications.