Monday, 23 June 2014

First user reports on Oxford Nanopore MinION!

After the start of the early access program, the sequencing community is waiting for the first results and comments on the MinION platform by Oxford Nanopore. This sequencer promises to revolutionize the field and is the first nanopore based sequencer that have reached the market.

Nick Loman, one of the early customer has now reported the first results obtained on the new platform. It is a 8.5 Kb read from P. aeruginosa showing that MinION can produce useful data, even if the accuracy remains low. Analyses of a read by two bioinformatics researchers, who used different alignment tools and posted their results here and here, showed that the read is about 68 percent identical to the P. aeruginosa genome and has many errors, particularly gaps. Main issues seems to be in the basecalling software, but Oxford Nanopore is working hard to improve it. Accordingly also to Konrad Paszkiewicz, another early customer, the device itself is really robust and easy to use and the library preparation procedure is simple, resulting in low sequencing costs.
The mean read length seems to be about 10 Kb, but users reported even longer reads up to 40 Kb, covering the entire lambda genome used for testing. So the read length is really promising and place the mature MinION as a natural competitor to PacBio.
The use of MinION seems straightforward: after plugging the sequencer into a USB 3.0 port of a computer, it installs the MinKnow software suite. A program called Metrichor uploads the raw data – ion current traces – to the Amazon Elastic Compute Cloud, where base-calling happens, either 1D base-calling for unidirectional reads or 2D base-calling for bidirectional reads.
Overall, improvements have to be made to the base-calling software, reliability of the flow cells, and library shelf-life, and new software needs to be developed by the community to take advantage of the MinION reads.  Oxford Nanopore said a new chemistry will be available in the coming months, which might include some of these improvements.

In the meantime, many other early access users contacted by IS website are awaiting the arrival of reagents, are in the midst of burn-in, or have run their own samples but are not ready to talk about their results yet. So we are expecting many more data and comments and detailed estimation on platform accuracy and data production to be out in the next months! The new minion has fulfilled the excpection in this first test and there is a lot promising about this new technology...maybe a new revolution in the field is ready to come!

Other details can be found on this post on GenomeWeb.

No comments: