A P. aeruginosa serotype-defining single read from our first Oxford Nanopore run

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Loman, Nicholas; Quick, Josh; Calus, Szymon (2014): A P. aeruginosa serotype-defining single read from our first Oxford Nanopore run. figshare.

http://dx.doi.org/10.6084/m9.figshare.1052996
Retrieved 19:18, Oct 31, 2014 (GMT)

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Here is, I think, the first publically-available Oxford Nanopore read to be published. This came off our MinION instrument this morning (Wednesday 11th June). The DNA was derived from Pseudomonas aeruginosa strain 910 which originally came from hospital water. 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.

 

Comments (3)

  • No quality estimates, signal clarity, etc?   Pretty odd read, 71% identity, lots of cruft in between, spans O6.  Even assuming there's no good ref at NCBI, in reasonably conserved, aligned regions there's still a lot of mismatch.  Maybe phred 8-12 at best?   Sad that the first released sequence is nigh-impossible to analyze for quality.

    13/06/2014    by E. Aronesty

  • Of course, if, like PacBio, there's less bias, you can make a lot up with coverage.   Still love to get my hands on one of these.

    13/06/2014    by E. Aronesty

  • E. Aronesty -- if you want to analyse that sequence further, try an aligner like LAST, BLASR or NUCMER to get a full-length alignment. It's fairly typical for a single-direction read. Raw data at http://github.com/nickloman/nanopore/

     

     

    15/06/2014    by N. Loman

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