Le Bao, Daniel Elleder, Raunaq Malhotra, Michael DeGiorgio, Theodora Maravegias,
Lindsay Horvath, Laura Carrel, Colin Gillin, Tomáš Hron, Helena Fábryová, David R. Hunter and Mary Poss
Scientists present a computational method for detecting specific integration sites of endogenous retroviruses in a genome, even without the use of a reference genome. They use de novo clustering and statistical models and demonstrate the approach in a study of deer. Pippin Prep sizing was used to narrow the fragment size range to 300-330bp prior to sequencing on the Ion Personal Genome Machine.
Computation 2014, 2, 221-245