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Old 03-08-2012, 04:01 PM   #1
Zimbobo
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Default Cost/run on HiSeq 2500

Does anybody have an estimate of the cost per run on a HiSeq2500?
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Old 05-14-2012, 06:55 AM   #2
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Default HS upgrade

We were told 2500 cluster kit for PE is $1225; SR is $795. 200 cycle SBS is $1690, 50 cycle SBS is $465.

Has anyone yet upgraded and how is it working out?
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Old 05-16-2012, 12:30 PM   #3
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Well that would be great.
But that would be a per lane reagent cost below that for a lane of HiSeq 2000 reagents. Since the amount of sequence generated per unit time is similar for a 2500 vs a 2000 flowcell, I will speculate that the person feeding you this information is wrong.
But maybe Illumina is just planning to steal the wind from the Proton Torrent's sails. This would tend to have that effect.

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Old 05-16-2012, 12:53 PM   #4
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Quote:
Originally Posted by pmiguel View Post
Well that would be great.
But that would be a per lane reagent cost below that for a lane of HiSeq 2000 reagents. Since the amount of sequence generated per unit time is similar for a 2500 vs a 2000 flowcell, I will speculate that the person feeding you this information is wrong.
But maybe Illumina is just planning to steal the wind from the Proton Torrent's sails. This would tend to have that effect.

--
Phillip
These are the costs for the '2' lane (single sample) flow cell, in rapid mode run--39 hrs for 2x150. MiSeq equivalent. By our calculations, it costs more, but makes operation more flexible--hard on users who want short, single reads to have to go in on 2x100 nt run and be charged accordingly.

Hilary
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Old 05-16-2012, 12:58 PM   #5
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Our rep indicated a premium of ~15% per GB data vs. the HiSeq2000. That's exactly in line w/ HMorrison's prices, since it would take five runs (120GB per HiSeq2500) to equal a single HiSeq2000 (600 GB).
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Old 05-16-2012, 01:48 PM   #6
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Apparently I miscalculated.
Still I would pay 15% more to get a data set back in 27 hours, rather than 12 days.

Hilary, what does the "same sample" comment in your spreadsheet mean? Are the 2 lanes in the flow cell loaded from a single source?

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Old 05-16-2012, 11:13 PM   #7
james hadfield
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Hi all I think the clustering is going to need to make use of current fluidics. It would be surprising if the $50,000 cost included new fluidics. If this is the case then I am not sure there is space to squeeze in all the reagents necessary to perform different run types. I guess we'll have to wait and see.

It would not be a big hardship to have to run the same run on both sides. The upgrade could be what many core facilities are looking for to get additional flexibility.

I posted a bit about the Proton install at BCM and HiSeq 2500 rapid runs on my blog...http://core-genomics.blogspot.co.uk/...me-in-day.html
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Old 05-21-2012, 12:02 AM   #8
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Quote:
Hilary, what does the "same sample" comment in your spreadsheet mean? Are the 2 lanes in the flow cell loaded from a single source?
Yes, from what Illumina's told us earlier this year, clustering will be performed on the Hiseq2500 and the same sample (or pool of samples) will be sequenced on both lanes.
I guess the sample (or pool of samples) will be loaded on the paired-end rack at the beginning of the run.
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Old 05-21-2012, 02:40 AM   #9
james hadfield
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This is exacty what I have heard as well. The same pol of samples will need to be rn on both lanes of the 2 lane flowcell. Has anyone seen a flowcell yet? I mocked on up for my blog last year, but have not seen a real one yet.
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Old 05-24-2012, 06:04 AM   #10
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Quote:
Originally Posted by pmiguel View Post
Apparently I miscalculated.
Still I would pay 15% more to get a data set back in 27 hours, rather than 12 days.

Hilary, what does the "same sample" comment in your spreadsheet mean? Are the 2 lanes in the flow cell loaded from a single source?

--
Phillip
Yes, although there are two 'lanes' they have to be the same sample--I think loaded from the same port. Sorry for the delayed response. Have been fighting with the FLX (and about to give it up).
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Old 08-22-2012, 06:30 PM   #11
Patincle
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Default HiSeq 2500 units delivered

Does anyone know how many hiseq2500 units have been delivered?
Has BGI upgraded their 127 hiSeq 2000s? Anyone?
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Old 12-17-2012, 10:23 AM   #12
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We just got our machine upgraded to a 2500. Validation runs went great and we will be running two FCs today on Rapid Mode! Nice not having to wait to fill FCs when odd read lengths are requested. There is data available on the Illumina BaseSpace for anyone to take a look.

Cost is as below (list prices):
SBS (50 cyc.) = $465
CLuster kit for on-board clustering = $795
cBOT clustering (additional) = $400

So for a 50bp (2 lane) rapid run ~300 million reads
If done on board = $1165
If cBOT clustering done = $1660
Per lane = $830

For 100bp paired-end, kit prices are as blow:
SBS (200 cyc.) = $1690
CLuster kit for on-board clustering = $1225
cBOT clustering (additional) = $400
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Old 04-02-2013, 08:07 PM   #13
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Quote:
Originally Posted by HMorrison View Post
These are the costs for the '2' lane (single sample) flow cell, in rapid mode run--39 hrs for 2x150. MiSeq equivalent. By our calculations, it costs more, but makes operation more flexible--hard on users who want short, single reads to have to go in on 2x100 nt run and be charged accordingly.

Hilary
How to calculate the per run cost? Thanks
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Old 01-08-2014, 10:19 AM   #14
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After looking through this thread I am still at loss as to what is the cost of the entire run on 2500 or 2000. My problem is that my libraries have to be sequenced with my custom sequencing primers, that is my samples cannot be pooled with other samples that use standard sequencing primers. The libraries run fine on MiSeq (2x100 PE) with these custom sequencing primers, but I need a much higher output than a few gigs per run. Thus, for 2500 I would nee to buy a two lane run, but on 2000 I would have to buy an 8-lane run, correct? So what average cost I should expect from a commercial provider (I need only fastq datasets)?
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Old 01-08-2014, 11:14 AM   #15
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Quote:
Originally Posted by yaximik View Post
So what average cost I should expect from a commercial provider (I need only fastq datasets)?
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/

Last edited by GenoMax; 01-08-2014 at 11:18 AM.
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Old 01-08-2014, 03:02 PM   #16
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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/).
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Old 01-08-2014, 03:38 PM   #17
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Quote:
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
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Old 01-08-2014, 03:57 PM   #18
yaximik
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Quote:
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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Old 01-08-2014, 04:02 PM   #19
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Quote:
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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Old 01-08-2014, 04:16 PM   #20
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Quote:
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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