As before, full run throughput in gigabases (billion bases) is plotted against single-end read length for the different sequencing platforms, both on a log scale. Yes, I know a certain new instrument seems to be missing, hang on, I’m coming back to that…
Earlier this week, the first paper was published describing the use of Oxford Nanopore MinION data to solve a biological question. The paper, entitled “MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island” came out in Nature Biotechnology (ReadCube link).
I was a reviewer for this manuscript. I have posted my two (signed) review reports on publons. As data and code were made available by the authors (as it should be), I made a (mostly successful) effort to reproduce the computational part of the paper. After I was done with the review report of the second version I could not help myself to have a further look at some of the results. This led to me sending some plots to the authors, and one of these plots ended up becoming figure 1. This was a lot of fun to see in the final version.
Below are some excerpts of the review reports.
The one and only Oxford Nanopore talk at AGBT 2014 – with real data
Twitter started buzzing this morning at AGBT because researchers started getting confirmation emails from Oxford Nanopore regarding their application for the MinION Access Program (MAP). This timed well with the first talk discussing some serious data from the platform, by David Jaffe from the Broad Institute, entitled “Assembly of Bacterial Genomes Using Long Nanopore Reads”. Probably no coincidence…
David Jaffe’s highly anticipated talk showed data generated by Oxford Nanopore on their MinION from two bacterial genomes. One was a methylation negative E coli (the fact that it was methylation negative may have been significant, but he didn’t say). The second species was a Scardovia. 5 micrograms of DNA were sent to the company. Library prep consisted of fragmentation and adaptor ligation, basically the classical workflow. Nothing was said about the type of adaptors.
On the Oxford nanopore MinIon Access ProgramLet’s say you hear about this company that claims to have a revolutionizing clothes washer, and you get to try it out! For a refundable $1000, they will ship you a washer, and they have plenty of their special washing powder available, which they will happily sell to you. The thing is, though, the company hasn’t shown anyone how good it actually works, how fast it works, and how clean your clothes will become. Not just that, once you have the washer, you’ll need to first use it on dirty clothers they will send you, and you’ll have to send them back the results. Also:
Only after achieving “consistent and satisfactory performance” with the test samples will participants be allowed to run their own [clothes]
Would you buy that washing machine? I guess not.