Developments in high throughput sequencing – July 2016 edition

This is the fifth edition of this visualisation, previous editions were in June 2015, June 2014, October2013 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. Yes, I know a certain new instrument (different from last time) seems to be missing, hang on, I’m coming back to that…

Notable changes from the June 2015 edition

• I added the Illumina MiniSeq
• I added the Oxford Nanopore MinION. The read length for this instrument was based on the specifications for maximal output and number of reads from the company’s website. The two data points represent ‘regular’ and ‘fast’ modes.
• I added the IonTorrent S5 and S5XL. You may notice that the line for this instrument has a downward slope, this is due to the fact that the 400 bp reads are only available on the 520 and 530 chip, but not the higher throughput 540 chip, making the maximum throughput for this read length lower than for the 200 bp reads.

Developments in high throughput sequencing – June 2015 edition

This is the fourth edition of this visualisation, previous editions were in June 2014, 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. Yes, I know a certain new instrument seems to be missing, hang on, I’m coming back to that…

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.

Looking back at AGBT 2014

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.

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. 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.

Would you buy that washing machine?

On the Oxford nanopore MinIon Access Program

Nothing like a fancy new washing machine (source: wikimedia commons)

Let’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.

My take on the sequencing buzz at #ASHG2012

Image from Wikimedia Commons. (Buzz was a low-cost airline based at London Stansted operating services to Europe. It was sold to Ryanair.)

I am not attending the American Society of Human Genetics meeting in San Fransisco, but can’t escape the buzz it creates on twitter (hashtag #ashg2012). Strikingly, it is almost another AGBT when it comes to announcements from companies selling sequencing instrument. All of them had something new to bring to the floor. This post summarizes what I picked up from twitter and a few websites, and I give a bit of my perspectives on the respective announcements. I am focussing on technology improvements, especially with regard to read lengths, not so much on applications such as cancer resequencing panels.