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Old 02-23-2011, 02:28 AM   #1
NGSfan
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Default HiScan SQ dual layer scanning rumor

Hi fellow Illumina users,

We have been getting some hints from the sales rep and the Illumina technician that there is a possibility of an upgrade to allow for dual layer scanning of the flowcell in our HiscanSQ in the future. That would effectively double the sequencing capacity! Basically, giving us 1/2 of a HiSeq 2000.

Anyone else heard about this? Can it be confirmed? I get mixed responses from the Illumina people.

Also, the recent upgrades to the flowcell and chemistry - would these come to the HiScanSQ?


thanks for any tidbits you can share!
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Old 02-23-2011, 08:25 AM   #2
swanny
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I spoke with my customer in AL last week and they said there are two upgrades that will take place soon; one in march and one during the summer. I sell them their computer servers and storage devices. They said the first upgrade will triple the amount of data being generated and then over the summer, another 3x. In total, 9-10x the amount of data will be generated per run compared to now. Their 1PB of storage will soon be gobbled up by these advances. They have 6 Hiseq's now. Is this what you are talking about?
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Old 02-23-2011, 11:45 AM   #3
csc
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I wouldn't be surprised if this was true. Since the HiSeq derives its imaging system from the iScan, I would imagine that the HiScan should be capable of dual surface imaging with some minor retrofitting.

As for this supposed 9-10x increase in data, it sounds a little far-fetched. Currently the output is rated at about 200-250Gb per run. Illumina has said that internally they have achieved 1.3 Tb runs, but I believe this is already using the upgrades in question (wider flow cell channels, higher cluster densities of 800-1000K/mm2). This would "only" represent ~5x increase in output. If they do have a strategy for another 2x of output on top of this, it doesn't seem likely that it will be in most customer hands by summer (maybe early release beta sites). But then again, who knows...
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Old 02-24-2011, 07:33 AM   #4
pmiguel
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Quote:
Originally Posted by NGSfan View Post
Hi fellow Illumina users,

We have been getting some hints from the sales rep and the Illumina technician that there is a possibility of an upgrade to allow for dual layer scanning of the flowcell in our HiscanSQ in the future. That would effectively double the sequencing capacity! Basically, giving us 1/2 of a HiSeq 2000.
This would double the scanning time though, I guess. Also seems bizarre that a top mounted scanner could "focus through" the clusters on the top surface of the flow cell and not have that impact the quality of the scan.

Quote:
Originally Posted by NGSfan View Post
Anyone else heard about this? Can it be confirmed? I get mixed responses from the Illumina people.
This one seems too good to be true to me. But I hope it is...
Quote:
Originally Posted by NGSfan View Post
Also, the recent upgrades to the flowcell and chemistry - would these come to the HiScanSQ?
Yes, it should be. Our HiScanSQ was just installed. It uses HiSeq Cluster and SBS chemistry. Our 2x100 PE acceptance test run should complete today. It ran with the v1 chemistry, but the new software/firmware. Run time will be 6 days. Has anyone with a HiSeq done a run with the software/firmware upgrade yet? (I am not entirely sure these have been released yet--they may have been applied to our instrument to deal with some issues during installation of the instrument.)

--
Phillip
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Old 06-14-2011, 09:49 AM   #5
dakota
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Phillip,
how did your validation run turn out? I am trying to get a better feel for the HiScanSQ.
thanks!
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Old 06-14-2011, 11:08 AM   #6
pmiguel
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Hi Dakota,
The final validation run and the training run turned out quite well. They were both done using v. 1 chemistry. The validation run produce 46.1 gigabases of >=Q30 sequence reads. The training run produced 60 gigabases of >=Q30.

For the training run we made our own (DNA) Truseq libraries and used indexes.

Next we will try some RNA libraries and some unamplified DNA Truseqs

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