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  • #16
    yaximik, you can provide custom sequencing primers for single lanes of a HiSeq 2000. We do it all the time for our nextRAD markers. The University of Oregon sequencing facility is used to custom jobs, so check with them (http://htseq.uoregon.edu/).
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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    • #17
      Originally posted by SNPsaurus View Post
      yaximik, you can provide custom sequencing primers for single lanes of a HiSeq 2000. We do it all the time for our nextRAD markers. The University of Oregon sequencing facility is used to custom jobs, so check with them (http://htseq.uoregon.edu/).
      SNPsaurus is right - you can't share lanes with anyone, but you don't necessarily need to buy an entire flow cell (just depends on how much coverage you want). We'd be happy to help you find the right provider - just let me know.

      Shawn
      www.allseq.com
      AllSeq - The Sequencing Marketplace
      [email protected]
      www.AllSeq.com

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      • #18
        Originally posted by GenoMax View Post
        Here is an example cost estimator you can try (without having to contact anyone): [url]https://dugsim.net/estimate_cost[/url
        Well, that site does not provide the option I need, and when I tried to contact them by e-mail my request like went into a black hole. That sucks...

        But the opp to get multiple quoting is interesting, thanks!

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        • #19
          Originally posted by SNPsaurus View Post
          yaximik, you can provide custom sequencing primers for single lanes of a HiSeq 2000. We do it all the time for our nextRAD markers. The University of Oregon sequencing facility is used to custom jobs, so check with them (http://htseq.uoregon.edu/).
          Wow, I was told that one cannot run a different seqprimer on one lane in the HiSeq 2000 flow cell. That is an eye opener, how they do that.

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          • #20
            Originally posted by AllSeq View Post
            SNPsaurus is right - you can't share lanes with anyone, but you don't necessarily need to buy an entire flow cell (just depends on how much coverage you want). We'd be happy to help you find the right provider - just let me know.

            Shawn
            www.allseq.com
            Guys, you are asking a way to many questions in making a project. All I need is to find the cist of sequencing of pre-made libraries on available instruments and compare available options (cost per lane or run, and output).

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            • #21
              Originally posted by GenoMax View Post
              Here is an example cost estimator you can try (without having to contact anyone): https://dugsim.net/estimate_cost

              Following sites give you access to multiple providers for quotes:

              AllSeq: http://www.allseq.com/
              Genohub: https://genohub.com/
              Are the Duke prices for real? Or are they only for academic institutions?

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              • #22
                Originally posted by yaximik View Post
                Wow, I was told that one cannot run a different seqprimer on one lane in the HiSeq 2000 flow cell. That is an eye opener, how they do that.
                Does that mean you can put one exome and one rna on the same lane?

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                • #23
                  Originally posted by ymc View Post
                  Does that mean you can put one exome and one rna on the same lane?
                  I doubt it. Correct me if I am wrong, the hydraulic system is one for all lanes, so the same reagents (including primers) are going to all lanes. So different samples cannot be run at the same time, that is the flow cell cannot be shared. One certainly can pay per run with only as many lanes as wanted, but would not one lane run on HiSeq 2000 be less preferable for providers than a full 7 lane shared run? So either cost or waiting time got to absorb the difference, both going to be less favorable for those who deviate from standard set up.

                  What I found unexpectedly in my search is that 2 weeks run on 2000/2500 seems less favorable because of the drop in the quality as reagents are sitting on the machine too long. Although it can produce more output (up to 300 GB?), how much data is lost after filtering bad reads? One day run on 2500 can produce up to 60GB or 2x30GB. It is a bit more expensive per GB, but the quality got to be higher and less data are lost after filtering low quality reads. How drastic is the difference?

                  With an average $3.5K per lane the slow mode will produce 30x6=180GB in 2 weeks for about $21K. The same 30x6=180GB can be produced by 3 fast mode two lane runs for about 3x$6K=$18K in less than a week, but with much better quality. So how the amounts of data are compared after quality filtering?

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                  • #24
                    High-output flowcells for the Hiseq are prepared on an ancillary piece of equipment known as a cBot.
                    The cBot pulls reagents through each lane separately, including libraries and their associated sequencing primers, and thus it is quite possible to have multiple different projects on the same flowcell, with each lane theoretically able to have its own sequencing primer or mix of primers. If you couldn't have multiple samples across the lanes of a flowcell, the whole operation would not be eve close to cost effective.
                    Where you would run into trouble is the turn-around chemistry, which happens onboard the Hiseq and does have all lanes pulling out of the same read2 primer mix. One could, again theoretically, spike in another primer in this tube and you might be able to get a custom read 2. Or you could just replace this tube completely with a tube of your own primer mix, assuming all 8 lanes require the same primer(s).

                    The overall drop in quality over a 10 day run is negligible for a library of good quality and a lab that knows how to run their sequencer. While it is true that the Rapid mode has less of a Q score drop over the length of its run (generally speaking, again assuming proper libraries and usage) the overall drop in quality is more of a technicality than an actual data analysis issue.

                    If you're paying more than $3k per lane for high-output on the Hiseq I think you're being overcharged. I've attached a price breakdown showing what I charge for academic users and the associated cost per M reads and Gbp.
                    My average high-output mode gives 38x8=304Gbp over 10 days for a little less than $19k. The same amount of data from a Rapid (with the same read lengths) would take 5 runs for a little more than $20k
                    You will always pay a penalty for Rapid mode runs.
                    Attached Files

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                    • #25
                      Originally posted by GW_OK View Post
                      High-output flowcells for the Hiseq are prepared on an ancillary piece of equipment known as a cBot.
                      The cBot pulls reagents through each lane separately, including libraries and their associated sequencing primers, and thus it is quite possible to have multiple different projects on the same flowcell, with each lane theoretically able to have its own sequencing primer or mix of primers. If you couldn't have multiple samples across the lanes of a flowcell, the whole operation would not be eve close to cost effective.
                      Where you would run into trouble is the turn-around chemistry, which happens onboard the Hiseq and does have all lanes pulling out of the same read2 primer mix. One could, again theoretically, spike in another primer in this tube and you might be able to get a custom read 2. Or you could just replace this tube completely with a tube of your own primer mix, assuming all 8 lanes require the same primer(s).

                      The overall drop in quality over a 10 day run is negligible for a library of good quality and a lab that knows how to run their sequencer. While it is true that the Rapid mode has less of a Q score drop over the length of its run (generally speaking, again assuming proper libraries and usage) the overall drop in quality is more of a technicality than an actual data analysis issue.

                      If you're paying more than $3k per lane for high-output on the Hiseq I think you're being overcharged. I've attached a price breakdown showing what I charge for academic users and the associated cost per M reads and Gbp.
                      My average high-output mode gives 38x8=304Gbp over 10 days for a little less than $19k. The same amount of data from a Rapid (with the same read lengths) would take 5 runs for a little more than $20k
                      You will always pay a penalty for Rapid mode runs.
                      If the cost of Rapid PE100 is $4,099, how can Duke offer $4,453???

                      Comment


                      • #26
                        Originally posted by ymc View Post
                        If the cost of Rapid PE100 is $4,099, how can Duke offer $4,453???
                        Oh I see. Your price is actually the academic price. So you are even cheaper than Duke.

                        Do you guys take non-academic projects?

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                        • #27
                          Wow, if you can do 60 GB for about $4К - I am your customer!

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                          • #28
                            @GW_OK Hope you have spare capacity available since everyone is going to want to send sequencing your way

                            Are those prices meant *only* for in-house academic customers? Are they per lane or per flowcell prices?
                            Last edited by GenoMax; 01-11-2014, 06:01 PM.

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                            • #29
                              Originally posted by yaximik View Post
                              Wow, if you can do 60 GB for about $4К - I am your customer!
                              I doubt GW_OK is guaranteeing that volume of data for the price. If your libraries are good quality then that number is a guide to output you can expect.

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                              • #30
                                Originally posted by ymc View Post
                                If the cost of Rapid PE100 is $4,099, how can Duke offer $4,453???
                                Everybody's got their own overhead and pricing structure. When I was looking to offload excess work a while back I was getting quotes of up to $5k a lane(?!)

                                Originally posted by ymc View Post
                                Oh I see. Your price is actually the academic price. So you are even cheaper than Duke.

                                Do you guys take non-academic projects?
                                I'm fairly certain I'm one of the, if not THE, cheapest cores around. We take all comers, but I'll have to go back and see what we're charging for-profits (if that's what your "non-academic" means)


                                Originally posted by yaximik View Post
                                Wow, if you can do 60 GB for about $4К - I am your customer!
                                As Genomax mentioned, 60GB is not a guarantee, more of a guideline.

                                Originally posted by GenoMax View Post
                                @GW_OK Hope you have space capacity available since everyone is going to want to send sequencing your way

                                Are those prices meant *only* for in-house academic customers? Are they per lane or per flowcell prices?
                                I've had to turn away business before, which I hate doing (but when you're 4 months backlogged...) We're generally very accommodating for small projects. My in-house prices are cheaper, actually. What I posted is what you'd be charged as an academic researcher walking in to my core off the street. Hiseq is per lane, Rapids are per flowcell, Rapid Splits are per lane, Miseq is per flowcell (of course).

                                Originally posted by GenoMax View Post
                                I doubt GW_OK is guaranteeing that volume of data for the price. If your libraries are good quality then that number is a guide to output you can expect.
                                Precisely.


                                If you're interested in having some work done my contact info is on my (currently outdated) core website:
                                http://omrf.org/research-faculty/cor...on-sequencing/

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