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  • #31
    From: http://www.illumina.com/systems/hise...lications.html

    The HiSeq 3000/HiSeq 4000 Systems deliver the highest daily throughput and lowest price per sample for multiple applications, species, and sample types, providing an ideal solution for production-scale sequencing labs.
    Looks like no restrictions on sample types for 3000/4000.

    Comment


    • #32
      Originally posted by HeinKey View Post
      #SNPsaurus:
      I assume it will be 2x 150 bp in 3.5 days.
      2.1 to 2.5 billion clusters per flow cell, in a 2x150 bp run is 630 - 750 Gb.
      With a speed >200Gb per day a 2x 150 bp run will take 3.5 days.

      I wonder if we can upgrade the 2500 V4 machine to a 4000 version...
      Dumbass Question Alert, but does 2.1 billion clusters = 2.1 billion reads? Or would that be 2.1 billion clusters and with PE be 4.2 billion reads?

      I guess my real question is on the HiSeq3000, how many reads do I get with 2x150bp PE?

      Thanks in advance...

      Comment


      • #33
        Originally posted by cement_head View Post
        Dumbass Question Alert, but does 2.1 billion clusters = 2.1 billion reads? Or would that be 2.1 billion clusters and with PE be 4.2 billion reads?
        Yes. That is how illumina counts them.

        Originally posted by cement_head View Post
        I guess my real question is on the HiSeq3000, how many reads do I get with 2x150bp PE?

        Thanks in advance...
        Here are published specs (I assume you are interested in total sequence rather than number of reads): http://www.illumina.com/systems/hise...fications.html

        Comment


        • #34
          Our sales rep claimed there are no single read cluster kits available (yet) for HS3000/4000. Can anyone confirm? Sounds like a strange decision (if true) to me.

          Comment


          • #35
            Originally posted by andibody View Post
            Our sales rep claimed there are no single read cluster kits available (yet) for HS3000/4000. Can anyone confirm? Sounds like a strange decision (if true) to me.
            That probably means "for the time being" ... as manufacturing is ramped up for new reagents/flowcells. Specifications list a 1x50 run, so single end kits may be coming in future (http://www.illumina.com/systems/hise...fications.html).

            Comment


            • #36
              Originally posted by GenoMax View Post
              Yes. That is how illumina counts them.



              Here are published specs (I assume you are interested in total sequence rather than number of reads): http://www.illumina.com/systems/hise...fications.html
              No, I'm interested in total number of reads to calculate coverage.

              So, what this (thread) is saying, is that for the same amount of money on a HiSeq2500 RR, if I did the run on a HiSeq3000 - I can potentially get >10x the amount of reads?

              HiSeq2500 360M reads

              HiSeq3000 4.2B reads

              Have I got this right? If so, this is amazing!

              Comment


              • #37
                That's not really so amazing. A HiSeq 2500 in High Output mode will give you more than 6X as many reads (2 billion is the spec for v4). Rapid Run isn't for people who care about cost-effectiveness.

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                • #38
                  My understanding is the the HiSeq 4000 per lane cost will be similar to the per lane cost of the HiSeq 2500. At our local facility, the per lane cost is similar for high-output or rapid run on the HiSeq 2500. So I would say roughly the same costs for:
                  HiSeq 2500 high-output 200M reads per lane (8 lanes per run)
                  HiSeq 2500 rapid run 180M reads per lane (2 lanes per run)
                  HiSeq 3/4000 320M reads per lane (8 lanes per run)
                  Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

                  Comment


                  • #39
                    There should be an exact max of clusters for HiSeq 3000/4000 defined by the number of microwells (325M as stated above?).
                    We're getting regularly 300M reads on the upgraded 2500. If 325M is correct, the increase is not very pronounced if the shortened run durations are not countered in.

                    Comment


                    • #40
                      Originally posted by andibody View Post
                      There should be an exact max of clusters for HiSeq 3000/4000 defined by the number of microwells (325M as stated above?).
                      We're getting regularly 300M reads on the upgraded 2500. If 325M is correct, the increase is not very pronounced if the shortened run durations are not countered in.
                      Are you sure you are comparing the same numbers (read, clusters, lanes, flow cell)? And for the HiSeq 2500 numbers are you talking about Rapid Run or V4 High Output?

                      The HiSeq 3000/4000 specs are 325M clusters per lane, which would be 650M reads per lane for paired end runs (using Illumina's method of counting).

                      The HiSeq 1500/2500 specs are 250M clusters per lane for V4 High Output (500M reads per lane). Our experience is pushing even slightly past 280M clusters per lane results in dramatic decreases in %PF and read quality.

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                      • #41
                        High Output.
                        True, it's more like 270-290M with Q>30.
                        Still, it's 'only' a 15% increase. (again, not countering in speed and evenness of cluster density).

                        Comment


                        • #42
                          Originally posted by cement_head View Post
                          No, I'm interested in total number of reads to calculate coverage.

                          So, what this (thread) is saying, is that for the same amount of money on a HiSeq2500 RR, if I did the run on a HiSeq3000 - I can potentially get >10x the amount of reads?

                          HiSeq2500 360M reads

                          HiSeq3000 4.2B reads

                          Have I got this right? If so, this is amazing!
                          No, at best you may be looking at 1.5X the amount of sequence per $. (That 4.2B reads figure is likely for an entire flowcell.)

                          My guess is it will be slightly less than this as Illumina always combines an improvement in instrumentation/chemistry with an increase in reagent costs.

                          Plus there is the cost of the new instrument itself that may contribute to the cost of the service.

                          --
                          Phillip

                          Comment


                          • #43
                            The difference is even less if you compare HiSeq 2500 V4 to HiSeq 4000. The HiSeq 4000's specs claim 4.3-5B reads vs up to 4B reads on a HiSeq 2500. After factoring in instrument and overhead costs I would imagine that pricing for the 4000 runs may be higher for the first 6-12 months.

                            Comment


                            • #44
                              Originally posted by kcchan View Post
                              The difference is even less if you compare HiSeq 2500 V4 to HiSeq 4000. The HiSeq 4000's specs claim 4.3-5B reads vs up to 4B reads on a HiSeq 2500. After factoring in instrument and overhead costs I would imagine that pricing for the 4000 runs may be higher for the first 6-12 months.
                              Yes, I think maybe the main benefit from the 3000/4000 over a 2500-1T running v4 chemistry would be less worries about overclustering a flow cell. And that is big--on a psychological level. But I think most cores have systems in place that either make this rare or just leave it up to the customers to send correctly titred libraries.

                              --
                              Phillip

                              Comment


                              • #45
                                Increased throughput (reduced run time) appears to be the main thing. Would be nice if it translates to reduced costs but for that I think they need some serious competiton (BGI, not PII...).

                                Hiseq2500: 450-500 Gb, 6 days 4000: > 400 Gb/day

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