Oxford Nanopore MinION

Nanopore sequencing is the ‘new wave’ of sequencing technology. This moves away from sequencing-by-synthesis or detecting the incorporation of bases by semiconductors. Nanopore sequencing works by directly detecting the base composition of a DNA strand as it passes through the pore. In some ways it is similar to the Pacific Biosciences platforms, detecting a single strand of DNA, only it is a direct detection method and doesn’t rely on detecting fluorescence release from an incorporating nucleotide. The Earlham Institute has been in the MinION Access Programme (MAP) for some time and the platform is available for people to test in collaboration with us.

For more information on the MinION take a look at Oxford Nanopore’s website.

Oxford Nanopore MinION

The applications.

The MinION is a revolutionary piece of sequencing technology with a form factor that fits on the palm of your hand, and is powered by a laptop USB port. Consequently it will find a niche in a host of applications from rapid diagnostics to ‘in-field’ surveillance. Its long reads are not as accurate as the Pacific Biosciences platform, but can still be used for bacterial genome assembly and community profiling and offers the ability to detect modified bases.

The throughput.

The Mk1 MinION in ‘Fast Mode’ can yield 42Gb of data in 48 hours, consisting of about 4.4 million reads over 10kb in length. These figures are for 1D reads, which are not as accurate as the 2D reads that can be produced.

What we use it for.

As an experimental platform, we have been using it for Air-Seq - sequencing airborne particles captured in a Coriolis air sampler. EI have developed software for the MinION platform for QC purposes (NanoOK) and are active in the MinION Analysis and Reference Consortium (MARC).

Related reading.