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.
As it is out in the open that I was one of the reviewers of the ‘HGAP’ paper, I though I could as well make my review publicly available.
I have posted the review report (from February 2013) online at Publons. The review was actually done together with a PhD student in the group, Ole Kristian Tørresen (I like to do reviews together with others, it leads to better reviews and is a great learning experience for students!).
Here are the first few paragraphs. Enjoy!
Last month, a new paper appeared in BMC Bioinformatics, entitled “Automated ensemble assembly and validation of microbial genomes”. In it, the authors describe iMetAMOS, a module of the metAMOS package, for bacterial genome assembly. I was one of the reviewers (I signed my review), and post part of my review here. The full review can be found on publons.
iMetAmos workflow. From the paper, doi:10.1186/1471-2105-15-126
I signed my review because I believe in non-anonymous peer review (see Mick Watson’s “reviewer’s oath”).
I made my review available on publons, a platform to post pre- and post-publication peer-review reports after the article has been published, because I believe in open peer-review. EDIT Adam Phillippy, the senior author on the paper, posted the authors response to the review reports they received as a comment to review on publons!
I post the first part of my review here because it nicely summarises the paper and my (favourable) opinion of it. I’ll admit that I wrote these paragraphs of the review report with the idea of posting them to my blog 🙂
Earlier this year, I started a petition to ask Roche/454 Life Sciences to make the Newbler software (gsAssembly, gsMapper and Amplicon Variant Analyzer) open source. See this post for the background to the petition.
Source: Wikimedia Commons, by Marcus Quigmire
When I closed the petition, 162 people had signed it, see the PDF on figshare. During the Advances in Genome Biology and Technology (AGBT) meeting in Florida, I handed over the results of the petition to two Roche representatives, Dan Zabrowski, Head of Roche Sequencing Unit and Paul Schaffer, Vice President of Roche 454 Sequencing Business, see my blog post on the conversation I had with them.
Dan Zabrowski and Paul Schaffer promised me an official Roche response, and here it is (exclusively released through this blog): Continue reading
I attended, for the first time, the Advances in Genome Biology and Technology (AGBT) meeting in Florida. With this post, I intend to summarise my experiences of the meeting. I will not cover everything that happened at the meeting, but focus of the areas of my own interest.
A couple of weeks ago, I started a petition to ask Roche/454 Life Sciences to make the Newbler software (gsAssembly, gsMapper and Amplicon Variant Analyzer) open source. See this post for the background to the petition.
The results are in, see the PDF on figshare. 162 people have signed the petition. Many thanks to all of you!
This week, I attended the Advances in Genome Biology and Technology (AGBT) meeting in Florida, and on Thursday I handed over the results of the petition to two Roche representatives, Dan Zabrowski, Head of Roche Sequencing Unit and Paul Schaffer, Vice President of Roche 454 Sequencing Business.
I had a half hour, very open and interesting discussion with Roche. Roche expressed their appreciation of the fact that we as a community voiced our concerns and wishes around Newbler. Roche occasionally picks up signals from researchers, but a petition like this was very useful for them as a much stronger signal of what we think about one of their products.
Dan Zabrowski told me Roche is committed to fully support access to the Newbler software even after the 454 Life Sciences shutdown. They will take the request for open source access to the code seriously, and promised to come with an official response somewhere in the coming weeks. They did not hint at what that response would be, which is understandable.
I want to thank Dan Zabrowski and Paul Schaffer for giving me time to explain the background and hand them the results. I also again want to thank all of you who signed the petition. We may collectively have made a difference. Keep an eye out on my twitter feed and this blog for the official Roche response!
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.