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  • Is US$9600 cheap for one flow cell 2x100 rapid mode on HiSeq 2500

    I got a quote like this just for sequencing not including library prep or target capture. That's about 50-60Gb data according to the spec.

    Is this reasonable? Can I get a quote significantly cheaper than that?

    Thanks

  • #2
    It seems wrong to do this because I know that Genohub is a frequent answerer, but genohub is a fairly good tool to answer this specific question:

    Find and order next-generation sequencing services based on your project specifications. Receive instant quotes with guaranteed quality and turnaround time.


    You state sample numbers, number of reads (or coverage), preparation, and then it will spit out a list of current service providers and their asking price.

    Comment


    • #3
      Originally posted by gringer View Post
      It seems wrong to do this because I know that Genohub is a frequent answerer, but genohub is a fairly good tool to answer this specific question:

      Find and order next-generation sequencing services based on your project specifications. Receive instant quotes with guaranteed quality and turnaround time.


      You state sample numbers, number of reads (or coverage), preparation, and then it will spit out a list of current service providers and their asking price.
      Thanks for your reply. I am aware of genohub. But I want to know if my quote is way off or not before I try their service.

      Comment


      • #4
        Originally posted by ymc View Post
        Thanks for your reply. I am aware of genohub. But I want to know if my quote is way off or not before I try their service.
        You don't need to pay to use genohub. You may need a login, but you can get quotes without any obligation. If you're not prepared to go that far, you're basically asking someone to solve your specific case and not teach you how to solve the more general case -- you might as well just be ignorant to other quotes and pay the $9600.

        Comment


        • #5
          Try the Duke University sequencing estimator here: https://dugsim.net/ No account required.

          For one flow cell no library (international institution) estimate seems to e ~$4500 for a rapid 2 x 100 PE flowcell.

          Comment


          • #6
            Originally posted by GenoMax View Post
            Try the Duke University sequencing estimator here: https://dugsim.net/ No account required.

            For one flow cell no library (international institution) estimate seems to e ~$4500 for a rapid 2 x 100 PE flowcell.
            wow. then i do get ripped off. thanks for your reply.

            Comment


            • #7
              Originally posted by ymc View Post
              wow. then i do get ripped off. thanks for your reply.
              Turnaround time, data transfer, and a few other things are also important and will impact the price. If you've been quoted for a single lane run next week with basic QC / mapping, and data shipped a week later, maybe $9600 isn't so bad.

              Comment


              • #8
                Originally posted by GenoMax View Post
                Try the Duke University sequencing estimator here: https://dugsim.net/ No account required.

                For one flow cell no library (international institution) estimate seems to e ~$4500 for a rapid 2 x 100 PE flowcell.
                I just signed up genohub. How come I feel the Duke interface makes more sense than genohub?

                Comment


                • #9
                  Hi all,

                  Thought I'd respond here. There are 3 ways to connect with NGS service providers on Genohub:

                  Shop by Project: Enter the number of reads or coverage you need and we automatically calculate the "amount" of sequencing you need. You can filter by read length and platform after the results are displayed. Shop by project is good for users who don't have a specific platform in mind and are not sure about the "amount" of sequencing they need.

                  Shop by Technology: Use this interface if you know exactly what you're looking for. For example, if you are looking for the price and turnaround time for a 2x100 HiSeq 2500 lane, this interface is easy to use. You can filter your results by read type, length, platform, instrument.

                  Consultation by Genohub's Scientific Staff : If you're new to sequencing or would like to access a NGS service not currently on Genohub, just fill out this form and a scientist from Genohub will contact you (usually within hours) to offer their recommendation and refer you to providers that will be able to perform your sequencing, library prep and data analysis.


                  For the specific question on this thread, the cost of a lane of 2x100 rapid mode on HiSeq 2500, you can use the shop by technology page. I entered a search for this service and here are the results:
                  Find and order next-generation sequencing services. Receive instant quotes with guaranteed quality and turnaround time.


                  Note that this is for 1 lane. Ymc, is the $9,600 price you were quoted for 8 lanes or 2 lanes? Technically a flow cell of an Illumina HiSeq Rapid Run consists of 2 lanes, whereas a flow cell of an Illumina HiSeq consists of 8 lanes.

                  The Duke interface is well done. Other than that interface is only for Duke and Genohub is a matching service for providers all over the world, there are several other differences:

                  With Genohub, you can choose a sequencing/library prep/data analysis package, start your project and communicate directly with the service provider. You don't have to pay any fees for using Genohub. There is no obligation to move forward with a project until the provider has answered all your questions. Once you're happy, you can ship the samples to the provider. If during a project there are any changes, say you need data analysis service or would like to add some more samples, the provider can submit a "Project Adjustment" and change the scope and price of the project for you.

                  So why use Genohub? In addition to our intelligent project matching service, we are a trusted third party that provides a project interface to keep track of your projects, we make sure things are happening on time and that response times between provider and researcher are fast. At anytime you can check the status of your sequencing project on Genohub and receive instant notifications when there are changes. Notice that providers also list their maximum (worst case) guaranteed turnaround times for each service listed on Genohub. If turnaround time is more important for you, you can sort by that instead of price. We handle the payment process making it easy for transactions to occur internationally. Finally, at anytime during the project or even before the start of a project, Genohub offers scientific consultation and can help answer questions that come up.

                  Please feel free to email us at [email protected] if you have any questions or just respond to this thread !

                  - Genohub
                  Last edited by Genohub; 11-28-2013, 05:58 PM.

                  Comment


                  • #10
                    Originally posted by gringer View Post
                    Turnaround time, data transfer, and a few other things are also important and will impact the price. If you've been quoted for a single lane run next week with basic QC / mapping, and data shipped a week later, maybe $9600 isn't so bad.
                    This $9600 place can return data in 3-4 weeks including library prep (RNA+exome). Does that make it worthwhile?

                    Comment


                    • #11
                      Originally posted by ymc View Post
                      This $9600 place can return data in 3-4 weeks including library prep (RNA+exome). Does that make it worthwhile?
                      No one other than you can answer that; that's for you to decide. Have a look at the link that Genohub provided for comparison, which gives maximum turnaround times and prices.

                      Comment


                      • #12
                        I think Duke's price seems to make more sense. For PE100, I heard that the reagent cost is $2,915. If we assume the $700,000 HiSeq 2500 can last 5 years and each run takes one day, then the equipment cost for each run is only $383. If they sell it for $4,500, this left them $1,202 for other cost and profit. Seems quite reasonable to me. Am I missing something?

                        Comment


                        • #13
                          Originally posted by ymc View Post
                          I think Duke's price seems to make more sense. For PE100, I heard that the reagent cost is $2,915. If we assume the $700,000 HiSeq 2500 can last 5 years and each run takes one day, then the equipment cost for each run is only $383. If they sell it for $4,500, this left them $1,202 for other cost and profit. Seems quite reasonable to me. Am I missing something?
                          Well you are forgetting annual maintenance costs -- perhaps you can consider that part of 'other cost". Additionally the idea of a sequencing machine lasting 5 years is a laughable idea. Lately a sequencing center will be upgrading their machines every couple of years just to keep up with everyone else.

                          In any case academic pricing (which is what I presume Duke is reporting) is usually only loosely correlated with non-academic ("real world") pricing.

                          Comment


                          • #14
                            Don't forget about the IT infrastructure necessary to store and process all of the data. You can't just hook up an external hard drive to your laptop and call it a day. You need a pretty powerful computer and a couple of hours just to generate all of the demultiplexed FASTQ files.

                            Comment


                            • #15
                              Originally posted by westerman View Post
                              Well you are forgetting annual maintenance costs -- perhaps you can consider that part of 'other cost". Additionally the idea of a sequencing machine lasting 5 years is a laughable idea. Lately a sequencing center will be upgrading their machines every couple of years just to keep up with everyone else.

                              In any case academic pricing (which is what I presume Duke is reporting) is usually only loosely correlated with non-academic ("real world") pricing.
                              Thanks for your reply. So is assuming a sequencing machine to last two years more reasonable? Then $959 is in the equipment cost. The total becomes $3,874. Then it does look like Duke is not making much. Probably their pricing is just an academic deal?

                              Maybe around $7,000 is more reasonable for non-academic? I found some deals on genohub that is around $3,300 for one rapid mode PE 100 lane. That's pretty close to the $7,000 I estimated.

                              Comment

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