My review of “MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island”

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.
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My review of “Long-read, whole-genome shotgun sequence data for five model organisms”

Two days ago, a paper appeared in Nature Scientific Data by Kristi Kim et al, titled “Long-read, whole-genome shotgun sequence data for five model organisms”. This paper describes the release of whole-genome PacBio data by Pacific Biosciences and others, for five model organisms, Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, Arabidopsis thaliana, and Drosophila melanogaster, using quite recent chemistries.

Beyond the datasets described in the paper, Pacific Biosciences also released whole-genome data for the human genome, and very recently, for Caenorhabditis elegans using the latest P6/C4 chemistry. Check out PacBio devnet, also for data for other applications.

I think it is fantastic that Pacific Biosciences releases these datasets as a service to the community – and obviously to showcase their technology. Company-generated data often represents the best possible data, as it is done by people with very much experience with the technology. It remains to be seen if ‘regular’ owners of PacBio RS II instrument can reach the same level of data quality. Nonetheless, these datasets are very helpful for teaching (see my previous blog post), comparisons with other technologies (I wish a I could make time to throughly compare PacBio data to Moleculo data available from the same species), as well as development of new software applications.

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Our review of “Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data”, aka the HGAP paper

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!

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Developments in next generation sequencing – June 2014 edition

This is the third edition of this visualisation, previous editions were in October 2013 and December 2012.

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:

Developments in next generation sequencing June 2014

 

 

 

 

 

 

 

 

 

 

 

 

 

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Make Newbler open source: the Roche response and the future of Newbler

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

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

Make Newbler open source: petition results and the meeting with Roche

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

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…

The MinION from Oxford Nanopore. Source https://www.nanoporetech.com. Unshure about copyright...

The MinION from Oxford Nanopore. Source https://www.nanoporetech.com. Unsure about copyright…

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.

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