Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Can't wait for all this to go commercial

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


  • #2
    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?

    Comment


    • #3
      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.

      Comment


      • #4
        Thanks. Full length reads are what I'm hoping for and that fact that these are 2d reads bodes well for increased accuracy.

        Comment


        • #5
          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.

          Comment


          • #6
            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.
            Michael Black, Ph.D.
            ScitoVation LLC. RTP, N.C.

            Comment


            • #7
              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.

              Comment


              • #8
                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.

                Comment


                • #9
                  Nice summary of Clive Brown's talk at London Calling

                  Comment


                  • #10
                    videos of all the talks are up on the ONT website

                    Comment


                    • #11
                      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

                      Comment

                      Latest Articles

                      Collapse

                      • seqadmin
                        Strategies for Sequencing Challenging Samples
                        by seqadmin


                        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                        03-22-2024, 06:39 AM
                      • seqadmin
                        Techniques and Challenges in Conservation Genomics
                        by seqadmin



                        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                        Avian Conservation
                        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                        03-08-2024, 10:41 AM

                      ad_right_rmr

                      Collapse

                      News

                      Collapse

                      Topics Statistics Last Post
                      Started by seqadmin, Yesterday, 06:37 PM
                      0 responses
                      8 views
                      0 likes
                      Last Post seqadmin  
                      Started by seqadmin, Yesterday, 06:07 PM
                      0 responses
                      8 views
                      0 likes
                      Last Post seqadmin  
                      Started by seqadmin, 03-22-2024, 10:03 AM
                      0 responses
                      49 views
                      0 likes
                      Last Post seqadmin  
                      Started by seqadmin, 03-21-2024, 07:32 AM
                      0 responses
                      66 views
                      0 likes
                      Last Post seqadmin  
                      Working...
                      X