An Update on Our Nanopore Petition for Lex Nederbragt's Group

An Update on Our Nanopore Petition for Lex Nederbragt's Group

Dear Readers,

Here is an update regarding our petition to Oxford Nanopore.

To provide a little background, during AGBT, we learned that Lex Nederbragts groups request for early access to ONT Minion had been denied. We created an online petition to request the company to reconsider their decision.

Our primary motivation was to see an objective comparison between the long reads generated from PacBio and Oxford Nanopore, and Lex’s group has strong experience with the former technology. High error rate is one recurring feature of long reads from PacBio (and maybe Oxford Nanopore, based on these slides), but a number of bioinformatics tools have been developed to handle them. Someone with knowledge of those tools can compare the technologies fairly without getting bogged down with noisy long reads. Moreover, Lex is very comfortable with next-gen media (twitter, blog) and we will not have to wait for his paper to know what he found.

After getting a number of signatures, we were trying to figure out the best way to reach the company. We initially assumed that it would be hard to hear back from them, if we simply submitted the petition in a custom form on their website or sent to the ‘media’ email address. So, we requested Nick Loman by email for help to find someone, but he was not very interested in our efforts. Finally, we decided to do what we decided against in the first place, namely contact the company directly at their media address.

That was a pleasant surprise. Zoe McDougall, the communication director of ONT, was lightening fast in replying back to us. She explained that they had an overwhelmingly large number of requests for early access, and the company used a random selection to pick a subset from those. It is too late to change that decision.

But here is the good news !! She mentioned that the company will consider our petition for the next wave of invitees to MAP. We are planning to submit it at the end of next week, and you can still sign it here if you find our efforts worthwhile.

Here is the text for the petition -

Genome scientist Lex Nederbragt has been very active in the online community about sharing information on next-generation sequencing technologies. Also, his blog is generally considered fair, impartial and objective regarding various technologies. We are saddened to learn that his request for early access to Minion has been rejected. Since Nanopore sequencing is considered an important technology by many researchers (incl. us), we believe our knowledge and decision about the technology will be greatly enhanced by evaluation done by Dr. Nederbragt.

Although writing a comment is optional in the petition form, a number of others praised him strongly. Examples -

I completely subscribe this petition. If it wasn’t for the activity of Lex on Twitter, I wouldn’t know half of what I know about other single-molecule sequencing technologies.

Lex is a very fair& creative guy& charming in person; he would make an excellent early access participant

We at [removed] would love to see Lex get early access to the MinION platform as we’re sure he would provide a fair, balanced, interesting and articulate evaluation.

Written by M. //