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Old 05-14-2015, 11:13 AM   #1
lkral
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Default Can't wait for all this to go commercial

Looks like the sequencing world will be quite different in a year or two.

https://storify.com/OmicsOmicsBlog/london-calling-day-1
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Old 05-14-2015, 11:18 AM   #2
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If anyone at the nanopore conference is reading this, I would appreciate a bit more detail on mRNA sequencing. I assume this will be full length sequencing?
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Old 05-16-2015, 06:05 AM   #3
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Hi, it does not have to be full length sequencing. If you want some kind of quantification you would probably need to get all molecules to roughly the same size, otherwise there will be a bias towards short reads. What was shown was that it is possible to sequence mRNA/cDNA hybrids as 2d-reads.
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Old 05-18-2015, 09:46 AM   #4
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Thanks. Full length reads are what I'm hoping for and that fact that these are 2d reads bodes well for increased accuracy.
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Old 05-18-2015, 12:52 PM   #5
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We are about to do RNA sequencing on the MinION. I'll give a summary once we do.

I want to use the mark 1 though and haven't received it yet.
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Old 05-18-2015, 01:02 PM   #6
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Quote:
Originally Posted by lkral View Post
Looks like the sequencing world will be quite different in a year or two.

https://storify.com/OmicsOmicsBlog/london-calling-day-1
The sequencing world is always very different every year or two.
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Old 05-18-2015, 01:56 PM   #7
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Quote:
Originally Posted by NextGenSeq View Post
We are about to do RNA sequencing on the MinION. I'll give a summary once we do.

I want to use the mark 1 though and haven't received it yet.
Great, I'll look forward to it.
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Old 05-21-2015, 10:16 AM   #8
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The recommended way to do RNA-seq right now is to amplify first, it will be interesting to see how much input RNA is needed to do RNA/cDNA hybrid sequencing. By the way, the MinION is sort of commercialized already and will be quite competitive (compared at least to PacBio and Ion) once they get the speed up.
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Old 05-27-2015, 09:11 AM   #9
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Nice summary of Clive Brown's talk at London Calling

http://nextgenseek.com/2015/05/oxfor...ax-promethion/
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Old 06-16-2015, 11:13 PM   #10
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videos of all the talks are up on the ONT website
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Old 08-15-2015, 06:52 PM   #11
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Here's my summary, for what it's worth. People interested in this conference have probably seen this elsewhere:

On the 14th and 15th of May, 2015, Oxford Nanopore Technologies held their inaugural nanopore sequencing conference, London Calling.

The conference was set up to inform people about the current progress of Oxford Nanopore's first sequencing device, the muesli bar-sized, USB-powered MinION. Over 250 people were in attendance at the conference, representing 35 countries, including two from New Zealand: Nicole Moore from Environmental Science and Research, and David Eccles from the Malaghan Insititute of Medical Research. Over the course of two days, these attendees discovered how the MinION is quietly turning the world of sequencing inside out.

Everything needed for sample preparation and sequencing can fit into a single piece of checked luggage on an airplane. The MinION is robust enough to make it across unsealed roads to remote parts of Africa, where it has been used for sequencing on-location during the Ebola outbreak.

The MinION has also been put through its paces for tracking the traffic of organisms. Detection at the species level can be achieved in under 20 minutes of sequencing, and very subtle changes for the same species from different origins can be identified in less than an hour.

Clive Brown, Chief Technical Officer for Oxford Nanopore Technologies, gave a brief summary of what is to come in the near future of nanopore sequencing:
  • A fast mode for sequencing, allowing a human genome to be sequenced with high reliability in a 2-day run.
  • An improved Mk II sequencer, with six time the throughput and six times the run time of the first sequencer.
  • A clip-on sample preparation laboratory (Voltrax), allowing preparation and sequencing directly from blood in 20 minutes.
  • Time-based pricing, reducing the minimum cost of a single-molecule sequencing run to $50.
  • A 48-cell desktop sequencing device (PromethION) that can produce over 6 terabases of sequence per day, making sample preparation time the slowest part of the sequencing process.

Research laboratories, commercial organisations, and inquisitive individuals skilled in basic lab techniques can sign up for their own sequencing device through the MinION Access Program.

Nanopore sequencing is a disruptive technology, so is pretty hard to predict where it will go, but here are a few things that could happen with slight additional improvements in technology:
  • Automated environmental DNA sampling (e.g. in ponds, or at customs), allowing tracking / discovery of novel species
  • DNA sequencing that is about as quick as the quickest machine-based blood test (e.g. electrolyte testing), as a first point of call for when people get sick with some unknown bug
  • A shift from high-output short-read sequencing to massively-parallel long-read sequencing
  • Single contig de-novo genome assembly across long stretches of simple repeats
  • Amplification-free sequencing
  • Sequencing directly from RNA
  • Sequencing / discovery of non-canonical bases or epigenetic modifications
  • Protein purification via nanopore
  • Protein sequencing via nanopore
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