Nick Loman’s Talk on Nanopore Sequencing Using MinION at #UKGS2014

Nick Loman gave a first-ever talk presenting user generated Nanopore sequencing data from MinION.  (The first-ever look at Oxford Nanopore data, not generated by a user, was seen at last year AGBT .) Oxford Nanopore launched EAP late last year and possibly 100’s of users are part of the program and generating data from MinION. Nick Loman one of the early access program users presented his expereience with using MinION by Oxford Nanopore  at the UKGS2014 for clinical genomic applications. Here is the abstract of his presentation

Nanopore sequencing in clinical microbiology
Nicholas J. Loman, Instituteof Microbiology and Infection, University of Birmingham

Nanopore sequencing is a potentially disruptive genomics technology. Since May 2014, we have been participating in the Oxford Nanopore MinION(tm) access programme. The MinION(tm) is a USB powered and connected, portable single molecule sequencer, able to detect nucleotide words as they translocate through a biological nanopore. Event data is streamed in real time from the instrument and base called in the cloud. Real time analysis of sequencing data opens up new opportunities for the diagnosis of infectious diseases. In this talk I will relate our experiences in the MinION(tm) access programme, and characterise the platforms unique strengths and weaknesses. I will demonstrate our use of the MinION(tm) in a large hospital and community outbreak of Salmonella enterica serovar Enteritidis. Furthermore, I will discuss the potential future use of this platform for metagenomic diagnosis of infectious diseases.

Thanks to live tweeters, we have tweets summarizing Nick Loman’s talk. Here are the tweets storified. The biggest highlight of the talk is that Nick Loman will make two MinION datasets from E. coli K12 genome publicly available. Hurray!.. Surely, that will help address a lots of questions about Oxford Nanopore sequence quality, length and many more.

A few other highlights of the talk are

  • MinION can sequence really long reads.  The length of a read is limited by fragment size. MinION can possibly seqeunce reads up to 50kb
  • The tiny MinION can be sequenced for upto 72 hours producing 45,000 reads and worth of 277MB data.
  • MinION has 512 pores on a flow cell that can sequence. However, in current version 200–250 pores are active during sequencing experiment

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