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Old 01-20-2010, 03:10 AM   #1
james hadfield
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Default Illumina's new sequencers: HiSeq, GAIIx, GAIIe or iScan-Seq

So Illumina now have four sequencers available; GAIIx, HiSeq, GAIIe and iScan sequencing module (are they still doing this?). All offer exactly the same applications, biochemistry and data. But they differ in output.

The GAIIx, GAIIe and iScan seq module (? but I will not really consider it here any more) use the same flowcells but generate very different amounts of data. How do they do this? Is it a smaller camera or fewer tiles? Could it be lower cluster density? Or is the data slimmed down computationally? With any of these I suspect there may be possibilities to increase the data volumes on GAIIe to GAIIx levels but on a system that costs significantly less.

Which one would you buy? Do PIs really want this in their lab, I know egos can be large enough but wallets have a limit. Surely it makes more sense for groups to come together to get the output of HiSeq with only the overhead of one instrument, and a significantly easier one to operate based on my experience and current understanding of HiSeq.
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Old 01-20-2010, 11:44 PM   #2
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I suspect there may be possibilities to increase the data volumes on GAIIe to GAIIx levels but on a system that costs significantly less.
The Illumina documentation I saw said that you could upgrade a GAIIe to a GAIIx at any point so I suspect there is a hardware difference between the two - maybe just a limited imaging area or reagent volume?

I'm sure that eventually, like many previous technologies, this sort of sequencing will end up being the almost exclusive domain of high-throughput service providers. Whilst we're still in a state of flux though I think there is ample scope for departments or big labs to usefully run their own - though this isn's something to be undertaken lightly. We've certainly benefited from being able to get into the guts of our systems to both sort out problems and also figure out better ways of analysing our data. Turning sequencing into a commodity service only really becomes feasible when everyone wants the same thing and you can set up a big pipeline to pump the data out, and I'm not sure we're there yet.

I'm still interested to get more details about the HiSeq (do you guys actually have one?). The improved automation is potentially good if they've got it right. At least with a GAII you can get your hands on all of the main components and diagnose and fix problems for yourself. Given the amount of time one or other of our GAIIs has been out of action I'm not sure I'd want to swap them for a single HiSeq until I was really sure they'd ironed out all of the bugs.
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Old 01-21-2010, 07:49 AM   #3
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Default 5th NGS

Don't forget about their acquisition of Avantome in 2008. Illumina will be releasing a bench-top sized pyrosequencing machine later this year with ~2-3Gb output for the lower end of the NGS market.
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Old 01-22-2010, 12:46 PM   #4
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The Illumina documentation I saw said that you could upgrade a GAIIe to a GAIIx at any point so I suspect there is a hardware difference between the two - maybe just a limited imaging area or reagent volume?
I too suspect it may be a hardware difference between the GAIIe and GAIIx, though I believe it would be criminal if it were simply reagent volume. Recall when Illumina upgraded from GAI to GAII, they replaced the CCD with a new one that captured 4X the real estate per tile. The flowcell also grew in surface area at the same time. Despite that gain in surface area, the whole flow cell could be imaged with significantly fewer tile snapshots due to the increased area captured per tile with the large CCD. This in turn contributed to a considerable times savings in data collection. Since the current specs on the GAIIe and GAIIx indicate that both machines can run 35 cycles in "~2 days", what do you think might be going on here? Are two different cameras capturing the same amount of area (with same tile count), but at markedly different resolutions, such that the algorithms can only extract ~35-40% of the amount of cluster features on the GAIIe images that they can on the GAIIx images? Is there a change in the mag of the optics? Seems like if the GAIIx has higher mag, it would have to collect more tiles to take advantage of the full surface area. Is that the case, and the new GAIIx camera is just super fast? Is the "~2 days" for the GAIIe the same as the "~2 days" for the GAIIx?

Something is just not adding up here for me. If anyone hears anything about the specific hardware differences between the two models, I would love to hear it.
Thanks!
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Old 01-22-2010, 02:19 PM   #5
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I have been befuddled by the difference between the IIe and IIx myself. The data sheets for the two show them to be essentially identical, save for the instrument control computer. It is a little beefier on the IIx. They use exactly the same flow cells and reagent kits. They look identical; their dimensions and weight are identical. What the data sheets don't mention at all is the camera/optical system. Having given it some thought I believe that they must have put a much less capable, and much less expensive CCD in the IIe. The CCD is no doubt the single most expensive part on the whole sequencer, probably making up a significant fraction of the total cost of a GA. The question is how much is the difference. Does anyone have pricing information on the new IIx and IIe?
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Old 01-22-2010, 03:37 PM   #6
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The press release for the GAIIe states $250K (http://finance.yahoo.com/news/Illumi....html?x=0&.v=1). I am uncertain about a new GAIIx, probably in the $400K neighborhood. A significant difference if true!
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Old 01-23-2010, 09:55 PM   #7
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Quote:
Originally Posted by james hadfield View Post
So Illumina now have four sequencers available; GAIIx, HiSeq, GAIIe and iScan sequencing module (are they still doing this?). All offer exactly the same applications, biochemistry and data. But they differ in output.
As I known, the HiSeq use two flowcell and each flowcell carry the cluster in two sides, and use 4 camero , it is use two fold of reagent than GAIIx.
GAIIx and GAIIe use the same reagent but defferent output, I guess the most difference is the flowcell area.
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Old 01-27-2010, 10:31 PM   #8
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maybe the IMAGE system, the CCD on GAIIe is smaller than GAIIx.
Directly, different CAMERAs.
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Old 01-29-2010, 12:52 AM   #9
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I heard from someone that the HiSeq 2000 will not save the tile images - is this true? That would mean a lot of open source image analysis/basecallers development might die off... this is not good.
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Old 01-29-2010, 09:20 AM   #10
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NGSfan: I just finished training on our new GAIIx and the FAS said that hiSEQ will not store any of the image files and all will be deleted after RTA has processed them.
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Old 02-01-2010, 06:02 AM   #11
james hadfield
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The current default setup for a GAIIx is for image deletion once RTA has generated intensities, so no difference for a HiSeq. I suspect that open source image analysis is pretty thin on the ground anyway and base-callers should still have development opportunities from the RTA intensitites.

If you wanted to develope better image analysis I would guess you could set up a run to copy the images somewhere else. However it would not matter what sort of run (read-length, sample, number of tiles, etc) you were working with as most have clusters of similar size and distribution.

Illumina have made phenomenal advances in image analysis, that account for almost all the increase in sequence volume per run in the last couple of years. Ignoring read-length improvements in chemistry, a run generates 3-5 fold more PF clusters than in 2008. We averaged; 5.5M reads in 2008, 1M in J-J'09, 1.5MJ-D'09 and 1.7M so far in 2010. We are in the process of upgrading to SCS/RTA x.6 and hope to see 2.5M reads per lane.

There are still a large number of IPARs out there that were made obsolete because someone realised a standard PC could do image analysis and base-calling on the fly. If only they had thought of it 6 months earlier!
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Old 02-01-2010, 06:59 AM   #12
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Originally Posted by james hadfield View Post
There are still a large number of IPARs out there that were made obsolete because someone realised a standard PC could do image analysis and base-calling on the fly. If only they had thought of it 6 months earlier!
I'm going with the theory that this was a cunning plan to put some extra servers in the hands of the people doing the downstream bioinformatics. We're extremely grateful for the free servers we got to run our custom mapping pipeline, and I'm sure many other informatics groups are too!
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Old 02-02-2010, 06:07 AM   #13
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This is a good readl:

http://www.politigenomics.com/2010/01/hiseq-2000.html

As far I as can tell, you can save images, but I am not sure if you want to
do that considering you may need as much as 30Tb per run.
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Old 02-02-2010, 04:15 PM   #14
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With regard to the differences between GAIIx and GAIIe; our Illumina rep tells us that 'nobody knows, not even us'. I'm sure they're not keen to specify the cause of the throughput difference. Perhaps the GAIIe is just a "GAII" rather than "GAIIx"... although I haven't really looked at the projected throughput for the 'e'.

Illumina is also offering trade-in deals on the HiSeq from the GAII/x... it has (jokingly) been suggested that this might be a source of the GAIIe :-)
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Old 02-05-2010, 10:11 PM   #15
Xi Wang
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Default which one is newer, GAIIx or GAIIe

I'd like to know which one is newer, GAIIx or GAIIe. Thanks.
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Old 02-06-2010, 05:13 AM   #16
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I'd like to know which one is newer, GAIIx or GAIIe. Thanks.
The GA IIe is newer. It is built in the same enclosure and has the same fluidics as the IIx. I spoke with an Illumina Regional Manager yesterday and he confirmed that the IIe has different optics than the IIx and in his words "a smaller field of view". The IIe can collect only ~40% of the data that a IIx can, but the IIe costs only half as much as a IIx (~$250,000 USD vs ~$500,000).

The operational costs for the two instruments is identical. The library preparation, cluster gen and sequencing kits and protocols are identical. This means that the cost/read or cost/bp of the IIe will be ~2.5X higher than the IIx.

The IIe is meant for researchers whose budgets and sequencing requirements are smaller.
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Old 02-06-2010, 05:20 AM   #17
Xi Wang
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Originally Posted by kmcarr View Post
The GA IIe is newer. It is built in the same enclosure and has the same fluidics as the IIx. I spoke with an Illumina Regional Manager yesterday and he confirmed that the IIe has different optics than the IIx and in his words "a smaller field of view". The IIe can collect only ~40% of the data that a IIx can, but the IIe costs only half as much as a IIx (~$250,000 USD vs ~$500,000).

The operational costs for the two instruments is identical. The library preparation, cluster gen and sequencing kits and protocols are identical. This means that the cost/read or cost/bp of the IIe will be ~2.5X higher than the IIx.

The IIe is meant for researchers whose budgets and sequencing requirements are smaller.
Thanks, kmcarr. I think it's just the market strategy of Illumina.
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Old 03-11-2010, 08:29 AM   #18
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Default HiScan

The iScan-Seq is being released in April and it will have the throughput of the current GA-II. The name has been changed to the HiScan since the "innards" are based on the HiSeq.
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