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  • #76
    Originally posted by repogue View Post
    Re: jrbell71: as far as I know, the Life panels are not compatible with running on MiSeq (some people are trying to work out protocols I believe). Also, since the gene panels are small (about 13 kb cumulative sequence), the MiSeq would be overkill as it gives way more sequence than necessary.

    Re: snetmcom: The main driver is good quality sequence for mutation detection. We don´t need a very rapid turnaround. A good depth of coverage, and relatively straightforward analysis would be nice!

    Thanks.
    Agree on the quality of the Illumina data. It is quite accurate. Illumina has the homopolymer run, and in my experience a higher frequency of insertion and deletions.

    And yes, people are working on cross-platform panels that our interoperable. We currently have a few panels in beta testing that work on both Illumina and Ion Torrent with good results. The short of it, it is possible to do with careful attention to platform differences and sequence error profiles. Each assay needs careful characterization of its systematic differences in performance between the platforms. We have one methodology publication in pre-press production which should be out next month describing the general approach, and an expanded article on the method for interplatform interoperability with amplicon panels in the upcoming year.

    -Tom

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    • #77
      Originally posted by thomasblomquist View Post
      Agree on the quality of the Illumina data. It is quite accurate. Illumina has the homopolymer run, and in my experience a higher frequency of insertion and deletions.
      Huh??? That's backwards from my experience; did you mean "Ion" where you wrote "Illumina"?

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      • #78
        Originally posted by krobison View Post
        Huh??? That's backwards from my experience; did you mean "Ion" where you wrote "Illumina"?
        Oops. Yes. Ion has the homopolymer issue.

        Illumina is awesome data quality. Still we will keep Ion torrent for lower volume quicker turn around for more acute dx panels.

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        • #79
          Is Proton 2 chip a vaporware?

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          • #80
            Originally posted by ymc View Post
            Is Proton 2 chip a vaporware?
            From what I have heard it is getting released soon, they say end of this year, so maybe Feb next year . But the reps are saying 40-50 Gb of sequence now instead of the 100 Gb sequence it was initially marketed as. And read lengths are still only 100 bp instead of the 400 that marketing was spouting. It is getting more and more disapointing (since my lab has a proton).

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            • #81
              Originally posted by Jeremy View Post
              From what I have heard it is getting released soon, they say end of this year, so maybe Feb next year . But the reps are saying 40-50 Gb of sequence now instead of the 100 Gb sequence it was initially marketed as. And read lengths are still only 100 bp instead of the 400 that marketing was spouting. It is getting more and more disapointing (since my lab has a proton).
              I agree with Jeremy that this probably isn't 'vaporware', but it has definitely been delayed (10 months and counting...) In terms of output, Ion Torrent is now officially saying it will launch with 32Gb of output per run, climbing to 64Gb over a ~12 month period.

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              • #82
                Yeah IonTorrent is saying that for a year now. IonTorrent says a lot of things, but do they deliver? How is the Avalanche coming along?

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                • #83
                  Originally posted by Zaag View Post
                  Yeah IonTorrent is saying that for a year now. IonTorrent says a lot of things, but do they deliver? How is the Avalanche coming along?
                  Ion Isothermal Amplification Chemistry (formerly known as Avalanche)

                  This new, single-tube chemistry delivers isothermal amplification of 500 bp library templates in as little as 30 minutes. The complete template preparation process takes just two hours, and will enable the industry's fastest benchtop sequencing workflow, by far.
                  - See more at: http://ioncommunity.lifetechnologies....BTJ8mb0N.dpuf

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                  • #84
                    Originally posted by Zaag View Post
                    Yeah IonTorrent is saying that for a year now. IonTorrent says a lot of things, but do they deliver? How is the Avalanche coming along?
                    It was announced today at Ion World that customers will get early access to Avalanche next month with general availability early next year.

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                    • #85
                      Good to see that they are kicking. Hope it all ends well and we see something good delivered in Q1

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                      • #86
                        I'll keep my fingers crossed! Good to see that the avalanche is (finally) becoming available..

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                        • #87
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                          • #88
                            could post any links considering those avalanche news or presetnations?

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                            • #89
                              Can anyone update this question? We have a HiSeq2500 and a MiSeq here, and we have the opportunity to obtain an IonTorrent PGM essentially for free (we have to pay capital depreciation costs, but nothing else). Is taking this free* PGM even worth it considering we already have a MiSeq? Are there any applications for which the PGM shines over the MiSeq? Or will it just sit there because the MiSeq is as good as or better than the PGM across the board?
                              Last edited by ucpete; 01-28-2014, 05:12 PM.

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                              • #90
                                Originally posted by ucpete View Post
                                Are there any applications for which the PGM shines over the MiSeq?
                                The PGM is known for speed, decent read lengths (up to 400b) and not dealing too well with homopolymers. There's new chemistry on the horizon that might significantly improve the homopolymer issue.

                                Should you get one (more or less for free)? If you highly value quick runs (<1 day instead of 24 hours) and have lots of small targeted sequencing projects, it might be a good choice to add to your panel of instruments.

                                But nothing is truly free - be sure you have the time both to teach yourself how to use this new platform and to support it/keep it running.
                                AllSeq - The Sequencing Marketplace
                                [email protected]
                                www.AllSeq.com

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