Ashton, P.M. et al. Nat. Biotechnol. doi:10.1038/nbt.3103 (8 December 2014).

Long-awaited results from the early access program for Oxford Nanopore Technologies' MinION sequencer are beginning to reveal the practical potential for nanopore sequencing. Ashton et al. used the long MinION reads to resolve an antibiotic resistance 'island' in multidrug-resistant strains of Salmonella enterica that cause typhoid fever. The island contains repetitive elements that are challenging for short-read sequencing; an assembly based only on short-read Illumina data consisted of 86 fragments, or 'contigs', whereas a hybrid approach that also used MinION reads as scaffolds produced an assembly made up of just 34 contigs. The nanopore reads had a median length of 5.4 kilobases and a maximum length of 66.7 kilobases. The work demonstrates that the small sequencers could be used to help diagnose bacterial pathogens.