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-   -   Is US$9600 cheap for one flow cell 2x100 rapid mode on HiSeq 2500 (http://seqanswers.com/forums/showthread.php?t=36240)

ymc 11-27-2013 11:24 PM

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

gringer 11-28-2013 02:47 AM

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:

https://genohub.com/shop-by-next-gen...ncing-project/

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.

ymc 11-28-2013 06:15 AM

Quote:

Originally Posted by gringer (Post 123424)
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:

https://genohub.com/shop-by-next-gen...ncing-project/

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.

gringer 11-28-2013 12:07 PM

Quote:

Originally Posted by ymc (Post 123439)
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.

GenoMax 11-28-2013 12:26 PM

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.

ymc 11-28-2013 03:19 PM

Quote:

Originally Posted by GenoMax (Post 123476)
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.:eek: thanks for your reply.

gringer 11-28-2013 04:02 PM

Quote:

Originally Posted by ymc (Post 123488)
wow. then i do get ripped off.:eek: 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.

ymc 11-28-2013 04:04 PM

Quote:

Originally Posted by GenoMax (Post 123476)
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? :confused:

Genohub 11-28-2013 05:38 PM

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:
https://genohub.com/shop-by-next-gen...4bcc6c800bf101

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

ymc 11-28-2013 07:52 PM

Quote:

Originally Posted by gringer (Post 123491)
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?

gringer 11-28-2013 10:02 PM

Quote:

Originally Posted by ymc (Post 123497)
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.

ymc 12-01-2013 08:13 PM

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?

westerman 12-02-2013 12:23 PM

Quote:

Originally Posted by ymc (Post 125877)
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.

kcchan 12-02-2013 01:52 PM

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.

ymc 12-02-2013 09:48 PM

Quote:

Originally Posted by westerman (Post 126204)
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.

westerman 12-03-2013 10:38 AM

Quote:

Originally Posted by ymc (Post 126235)
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?

Probably. Academic pricing is strange because of how grants are handled and how central administration allocates funds. Actually academic pricing is not much different than how a company might *internally* charge itself for sequencing. Internal pricing certainly has little bearing on external-to-the-organization pricing.

AllSeq 12-04-2013 10:34 AM

Quote:

Originally Posted by ymc (Post 126235)
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.

As you can see, pricing runs can be tricky, and it is especially difficult to compare academic and commercial pricing. But the other thing to keep in mind is that the numbers you’re seeing are estimates. Most providers (especially commercial ones) will charge different prices at different times (based on instrument capacity) and for different projects (based on things like difficulty and long-term value of the customer).

The only way to know the actual price for your exact project on the exact terms you want is to contact the individual providers and give them all of the relevant information. They can then tell you if they have the capacity, how long it will take, and exactly what they will charge. The time consuming nature of doing this for more than one or two providers is the reason AllSeq created the Sequencing Marketplace. You describe your project once (using our online tools) and then have multiple providers (academic and commercial) bid on your project. Only those providers who have the interest and the capacity will be bidding, so you won’t waste time chasing down estimated prices that may or may not ever materialize.

Good luck and let us know what you end up doing.

Shawn
AllSeq

gringer 12-04-2013 12:28 PM

Quote:

You describe your project once (using our online tools) and then have multiple providers (academic and commercial) bid on your project.
Or use Genohub, which provides you with fixed prices first for a range of general use conditions, and then you can contact the provider directly with their pre-generated quote -- no time lost in waiting for bids. I guess the disadvantage of genohub is that it doesn't allow you to be completely specific about your needs (although the consultation option would probably work for that).

AllSeq 12-04-2013 01:41 PM

Quote:

Originally Posted by gringer (Post 126454)
Or use Genohub, which provides you with fixed prices first for a range of general use conditions, and then you can contact the provider directly with their pre-generated quote -- no time lost in waiting for bids. I guess the disadvantage of genohub is that it doesn't allow you to be completely specific about your needs (although the consultation option would probably work for that).

Using one of the various listing services out there is certainly an option. However, it’s very hard for a provider to list an accurate price when they don’t know all of the details (how many lanes, what sample type, sample shipment date, data delivery date, etc). For example, a provider can list a price for a single lane of 1X50bp reads, but if you only buy one lane, they’ll be hard pressed to fill the other seven lanes. The buyer either has to pay for the full flow cell, wait (maybe months) for the other lanes to fill up, or run a different configuration (like the popular 2X100bp). Therefore, you still need to communicate individually with each provider to make sure they’ll really be able to run your samples at that price, configuration and timeframe. If you’re only dealing with a couple that’s not so bad, but I wouldn’t want to do that with 40+ providers. That would take a lot longer than a streamlined bidding process.

And AllSeq (as well as most providers) will happily offer a free consultation to help researchers design the most efficient NGS experiment. Our team has helped hundreds of people do this.

Shawn

Genohub 12-04-2013 03:23 PM

100% accurate pricing is indeed not very straightforward but it's a problem we've put in a lot of effort addressing. As a result the prices on Genohub are actually quite accurate. As a client when you submit a project the provider has the chance to review the details specific to your project and submit adjustments if needed. It's quite an easy and streamlined process. There's no commitment on the part of the client until the samples are actually shipped. So far, the majority of submitted projects on Genohub haven't required any price adjustments.

The way we achieve this is by offering providers an easy and powerful interface to manage their listings, and by working with them to maintain accuracy. Providers can list per-lane pricing, per-flow cell pricing, one-time offers, etc. and our software takes all of these into account to instantly calculate the best price based on client's requirements. Providers are also able to activate and deactivate individual services based on their capacity situation at the time.

Ultimately price is only one factor. We try to present as much information as possible to clients up-front, including things like available bioinformatics services, turnaround time, etc. In most cases that's sufficient but as a client you're free to submit your project to more than one provider and get more custom quotes, e.g. if you have very custom bioinformatics needs or have a multi-phase project with a mix of sample types.

We'd always love to hear your feedback and ideas on how to improve our service.

-Genohub


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