A first look at the Oxford Nanopore MinION sequencer

Oxford Nanopore's third-generation, single-molecule sequencing platform promises to decrease costs for reagents and instrumentation. After a two-year hiatus following the initial announcement, the first devices have been released as part of an early access program. We explore the performance of this platform by re-sequencing the lambda phage genome, and amplicons from a snake venom gland transcriptome. Although the handheld MinION sequencer can generate more than 150 megabases of raw data in one run, at most a quarter of the resulting reads map to the reference, with less than average 10% identity. Much of the sequence consists of insertion/deletion errors, or is seemingly without similarity to the template. Using the lambda phage data as an example, although the reads are long, averaging 5kb, at best 890±1,932 bases per mapped read could be matched to the reference without soft clipping. In the course of a 36 hour run on the MinION it was possible to re-sequence the 48kb lambda phage r...