What is our interest in nanopore?
We wear a couple of different hats in my research group. Part of the time we spend developing new data structures and methods for representing genetic variation, which is a subject of a future post. But we are also interested in applications of sequencing to problems in clinical microbiology. Anyone reading this blog is likely to have heard of the Oxford Nanopore MinION sequencer, and to be aware it is a USB-stick-sized single molecule sequencing machine that generates reads in real time. There are many obvious benefits to having a cheap, fast, portable, long read sequencer, especially in a clinical setting where you don’t want to wait until you have enough sick people to justify a MiSeq run. But for this analysis, we wanted to know how well whole-genome assembly works with nanopore data, and how close to a finished genome can you get. Of course, once you push the boundaries, it gets hard to define finished, as samples continue to evolve during culture, and there is no Heaven-sent Truth for us to use. However if we can get an assembly that is highly concordant with a high-quality polished/manually studied PacBio assembly, then I’m going to be happy.