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  • #16
    Originally posted by GW_OK View Post
    Called it! Called it!

    Holy sh_!

    "NextSeq"
    Looks like I'll have to eat my hat! Exciting news!

    Comment


    • #17
      Originally posted by aeonsim View Post
      What I'd like is some more detailed explanation of the 2-dye system the NextSeq 500 is using. I assume they provide C & A tagged with Red, T & A tagged with green & G untagged, thus C should be pure Red, T pure green and A ~ a 50:50 mix of green & red (orange) and G then undyed...
      Spec Sheet from ILMN:

      Comment


      • #18
        New patent on the exclusion amplification for the X. http://bit.ly/1j6sSll

        Just transport the dna fragments slowly and amplify quickly.
        Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

        Comment


        • #19
          Originally posted by GW_OK View Post
          Called it! Called it!

          Holy sh_!

          "NextSeq"
          I think you mean "Nailed it!" - really good call!
          AllSeq - The Sequencing Marketplace
          [email protected]
          www.AllSeq.com

          Comment


          • #20
            Originally posted by M4TTN View Post
            Interested to see that the cluster density specs are an order of magnitude lower on the 500 than the MiSeq. Is that an error?

            Quote from Illumina:
            (http://www.illumina.com/systems/next...fications.ilmn)
            * Install specifications based on Illumina PhiX control library at supported cluster densities (between 129 and 165 k/mm² clusters passing filter). Actual performance parameters may vary based on sample type, sample quality, and clusters passing filter.
            See flowcell pics on Twitter @nextgenseek
            Fat lanes = different optics
            Probably not a typo

            Comment


            • #21
              Originally posted by BBoy View Post
              See flowcell pics on Twitter @nextgenseek
              Fat lanes = different optics
              Probably not a typo
              Does fatter lanes = more reagents = more expensive per run?

              It also suggests massive potential for improved performance over time (by increasing cluster density).

              We just received a refurb MiSeq in December 2013, so I'm somewhat dismayed by the NextSeq500 release. However 250k is well out of budget.

              One wonders if the MiSeq will still get improvements. I notice from the HiSeqX spec sheet that they are now using ordered arrays. I wonder how much of an improvement this could yield on the MiSeq, which already has a very high cluster density.

              The two things I'd really like to see is MiSeq hit 100M clusters and the cost of reagents per run to halve.

              Comment


              • #22
                Originally posted by SNPsaurus View Post
                The rep at PAG said they planned on selling 4 "X boxes" in 2014--and had already sold 3 30 minutes after the announcement.
                That is insane.

                Comment


                • #23
                  I hope illumina will reconsider "10 to a pack" decision for X in future (there can't be more than a handful customers at that level and 3 are already on board).

                  More than a handful places can use one (or two) X's.
                  Last edited by GenoMax; 01-15-2014, 04:15 AM.

                  Comment


                  • #24
                    Originally posted by M4TTN View Post
                    Does fatter lanes = more reagents = more expensive per run?
                    Perhaps they are using slower flows to use relatively less reagents. Patent linked in #18.
                    Originally posted by M4TTN View Post
                    It also suggests massive potential for improved performance over time (by increasing cluster density).
                    This is analogous to "Intel's" business strategy. Release just enough "innovation" to remain a comfortable step ahead of competitors.
                    Last edited by GenoMax; 01-15-2014, 04:21 AM.

                    Comment


                    • #25
                      Originally posted by GenoMax View Post
                      Perhaps they are using slower flows to use relatively less reagents. Patent linked in #18.


                      This is analogous to "Intel's" business strategy. Release just enough "innovation" to remain a comfortable step ahead of competitors.
                      Interesting idea.

                      Indeed, the relative lack of competition in both CPUs and NGS is a concern for those doing research on a limited budget.

                      I'd like to see someone reverse engineer a flowcell and compete on reagent costs, but I doubt it will happen.

                      Comment


                      • #26
                        Originally posted by M4TTN View Post

                        It also suggests massive potential for improved performance over time (by increasing cluster density).
                        Maybe more "headspace" by driving scanning/optics?

                        Comment


                        • #27
                          Originally posted by Geneus View Post
                          Maybe more "headspace" by driving scanning/optics?
                          I'm thinking their cluster calling algorithm is not quite as robust and/or they're playing it safe with only two images to work with per cycle.

                          Comment


                          • #28
                            Originally posted by ECO View Post
                            Spec Sheet from ILMN:
                            http://bit.ly/1iOYN7e
                            Read that, it provides the basic information but not much more.

                            The one really stupid and highly annoying thing about the Hiseq X is the restriction to only sequence Human genomes (at the $1K 30x cost). It's an entirely arbitrary restriction to increase there profits and nothing else.

                            Especially seeing it sounds like it's a software based restriction which effectively means they're selling you hardware (expensive hardware) that they've purposefully crippled if you want to do anything other than Human genomes. Highly aggravating hopefully some of the groups that buy the instruments will come up with a work around or means of disabling this restriction, certainly the first service provider who can get a large (~3GB) non-human genome out for ~1K will have plenty of interested buyers (assuming Illumina contractually doesn't prevent this...).

                            Comment


                            • #29
                              Originally posted by aeonsim View Post
                              Read that, it provides the basic information but not much more.

                              The one really stupid and highly annoying thing about the Hiseq X is the restriction to only sequence Human genomes (at the $1K 30x cost). It's an entirely arbitrary restriction to increase there profits and nothing else.

                              Especially seeing it sounds like it's a software based restriction which effectively means they're selling you hardware (expensive hardware) that they've purposefully crippled if you want to do anything other than Human genomes. Highly aggravating hopefully some of the groups that buy the instruments will come up with a work around or means of disabling this restriction, certainly the first service provider who can get a large (~3GB) non-human genome out for ~1K will have plenty of interested buyers (assuming Illumina contractually doesn't prevent this...).
                              I agree this is a stupid restrictions. However, is there a lot of drive to do huge scale, medium depth, WGS on a species other than human? How many 30x mouse genomes can one need?

                              You aren’t going to get a de novo genome with 30x at a single fragment size, at least not one worth much. And the de novo sequencing must make up a tiny fraction of sequencing projects in the world. So, if Illumina is going to have some 5 different machines now, what the problem in having one machine dedicated to large scale human resequencing studies? Maybe the implementation is wrong, but I think the general idea is right, especially from a marketing perspective.

                              Comment


                              • #30
                                Originally posted by Wallysb01 View Post
                                I agree this is a stupid restrictions. However, is there a lot of drive to do huge scale, medium depth, WGS on a species other than human? How many 30x mouse genomes can one need?
                                I suspect that doing GWAS studies on mice, dogs, etc. could be of interest. It is nice to to have inbred lines but being able to sequence the outbred lines could produce interesting results that can be easily experimentally verified in ways that human experimentation is not allowed.

                                Now funding such a study might be difficult. It is one thing to say "$1000 to sequence yourself" versus "$1000 to sequence your pet".

                                You aren’t going to get a de novo genome with 30x at a single fragment size, at least not one worth much.
                                Agreed.

                                And the de novo sequencing must make up a tiny fraction of sequencing projects in the world. So, if Illumina is going to have some 5 different machines now, what the problem in having one machine dedicated to large scale human resequencing studies? Maybe the implementation is wrong, but I think the general idea is right, especially from a marketing perspective.
                                Yes, I think that is a good point. A year from now after the initial sales have slowed down then perhaps marketing will point towards other species.

                                Comment

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