Tips and tricks for the new Oxford Nanopore MinION user for plant genome sequencing: a short technical note

In the last decade a growing number of plant genomes have been obtained for species previously considered as non model species, thanks to the development of long read sequencing. The availability of bench sequencing devices such as the Oxford Nanopore Technologies (ONT) MinION has opened the way for in house sequencing in many labs. In this short technical note we aim at providing a few tips for handling the plant material, performing the DNA extraction, libraries preparation and sequencing run on a MinION platform. We further describe basic steps in obtaining a high quality base calling, delivering quality control metrics, visualizing the data with IGV and detecting structural variants if a reference genome is available. We hope this will be useful for colleagues interested in population genomics and in the discovery of structural variants in a variety of plant species