EpiGBS of L. pratensis from offspring of the Jena Biodiversity Experiment
The epiGBS protocol used is a further developed protocol based on the protocol of van Gurp et al. (2016, doi:10.1038/nmeth.3763). The main improvements are on the enzyme combination used and the use of a  wobble  adapter that facilitates the computational removal of PCR duplicates and a conversion control nucleotide that also allows easier Watson / Crick identification. For 348 samples, (Csp6I/NsiI) epiGBS libraries were created and sequenced on 4 Hiseq 2500 lanes. The data submitted here has been demultiplexed accoring to the species. Read groups in the short read headers indicate the plant ID. Barcodes required by the epiGBS pipeline (github.com/thomasvangurp/epiGBS) were uploaded to Zenodo (doi:10.5281/zenodo.1167563).