Long reads are here to rule. Thanks to Nick Loman from Birmingham UK, now we can have our first look at long reads from Oxford Nanopore. Nick Loman has tweeted and published on figshare the first long read from Oxford Nanopore MinION. It is a 8476 base long DNA sequence from Pseudomonas aeruginosa strain 910 produced by Nanopore’s MinION just this morning.
A genuine >8kb Oxford @nanopore read off our instrument THIS MORNING. And happily it’s actually useful for diagnosis! http://t.co/vKbbSiDNb6
— Nick Loman (@pathogenomenick) June 11, 2014
It is just a single read as of now. And at a first look the tweet does not tell much. We already know it can sequence this long reads. The highlight of the tweet lies in the second part of the tweet, which “actually useful in diagnosis”.
First Look at Oxford Nanopore Read (Credit: Nick Loman)
A quick BLAST search confirmed the origin of the first MinION read. Searching for a hit using BLAST (not megaBLAST) for somewhat similar sequences with blastn in “NCBI Chromosome Sequences” database yielded a ton of results from Pseudomonas aeruginosa.
The best results covered about 3151 bases of the read starting from about 2180th base to 4990th base. In the aligned part of the read there was 68% identity (2129/3151) with gaps covering about 15% (496/3151) of bases. BLAST is probably not the right approach and its gap penalty is not optimized for Nanopore reads. Full BLAST search results of Nanopore MinION read are available here. Save the BLAST server :) BLAST took close to 30 mins to run the search. [Update]: Thanks to Mark Chaisson, there is a better alignment of the read now. He aligned the read using blasr, the long read aligner developed for PacBio reads. Here is quick alignment stats from it.
- nMatch: 6499
- nMisMatch: 929
- nIns: 744
- nDel: 1390
- %sim: 67.96
Oxford Nanopore read alignment- top BLAST hit
Nick Loman also offered more detail on sample prep.
DNA was fragmented with Covaris G-Tube as per the Oxford Nanopore standard genomic library preparation protocol. The read maps to part of the P. aeruginosa O6-antigen determining region.
The sequenced read is not the raw the data. The so called wiggle file showing the current change as the DNA goes through the nanopore is the real raw data. Nick Loman also uploaded a wiggle file from Nanopore MinION. Simply put, the wiggles/Manahattan skyline looks beautiful.
And for those wondering what “raw” @nanopore event data looks like, here’s the accompanying wiggle plot of events: http://t.co/eILB199VdI — Nick Loman (@pathogenomenick) June 11, 2014
A wiggle-plot for the Oxford Nanopore read posted today demonstrating change in current (measured in picoamps) over time [1]. The total translocation time for this fragment was ~273 seconds.
Nick Loman has also shared the raw wiggle data on his github page. It seems Oxford Nanopore has also embraced HDF5 format for its sequencing data. Already, PacBio uses HDF5 format for its sequencing data and it is slowly gaining a foothold in other genomic applications.
@isugif https://t.co/cOOtanlnk2 in examples/ folder
— Nick Loman (@pathogenomenick) June 11, 2014
First Oxford Nanopore MinION Wiggles
[Update] More details about using Oxford Nanopore MinIONs have already started coming. A blog, Omic Frontiers, by the Exeter Sequencing Service has two detailed blogposts with pictures on using MinIONs. Check them out
Diary of a MinIon – Part 1 – Min Ion Access ProgrammeDiary of a MinIon – Part 2 – Configuration Tests
Omic Frontiers have pulled the blogposts. It is anybody’s guess that it might have violated NDA from Oxford Nanopore.
Oxford Nanopore MinION Timeline So far
Oxford-Nanopore-MinION
The first look at the data has come exactly two months since MinIONs reached the hands of Oxford Nanopore MinION early access program users. As part of the EAP program the researchers spent time learning to use the device during the so called “burn-in” period. After the burn in period, the researchers can try their proposed idea and publish as they like. That means this single read is just the beginning, we are about to see a whole lot of reads from interesting genomics applications.
In case you missed, here is the brief timeline of Oxford Nanopore Technologies’ MinION.
- February 2012: Oxford Nanopore Technologies Announces MinION and GridION at AGBT 2012
- November 2012: Oxford Nanopore’s MinION and GridION in the Wild at ASHG 2012
- February 2013: Oxford Nanopore Skips AGBT 2014, but privatley talks about why it is behind the schedule.
- October 2013: Oxford Nanopore Launches MinION Access Program at ASHG2013
- November 2013: Oxford Nanopore MinION Access Program Opens
- February 2014: A first look at Oxford Nanopore MinION data at AGBT 2014 & it selects the lucky researchers
- March 2014: Oxford Nanopore MinION Gets Ready for Shipping
- April 2014: MinION reaches the hands of researchers
And you might also want to read these
While accepting that these are relatively early data, at these low levels of accuracy and the indication from the AGBT talk that the errors had a serious systematic component it’s not clear how much utility these data have. If I were PacBio, I wouldn’t be overly concerned just yet.
Perhaps, Tim, for those that don’t know you should declare your commercial interest in this context.
Ok. Let me start you off Tim.
Your brother is Mike……
Mike is the President and CEO of…….
Take you time.
FYI, the Omic Frontiers blog posts are back online, as well as a few new posts too.