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Old 01-24-2018, 12:32 PM   #1
r.rosati
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Default Ion Torrent sequencers comparison

Hello,
so, now Thermo has 8 Ion Torrent models for sale (for future reference: PGM, PGM-Dx, Proton, S5, S5 XL, GeneStudio S5, GeneStudio S5 Plus, GeneStudio S5 Prime).

I'm trying to wrap my head around the differences and I've made a quick spreadsheet from info I gathered from their website.

I thought I'd share, also because I'd enjoy a double-check from more experienced users, and I still miss some data.

The spreadsheet can be viewed here:
https://docs.google.com/spreadsheets...it?usp=sharing

Cells in orange are missing/uncertain.

Any corrections and new data are welcome. Thanks!
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Old 02-02-2018, 04:21 PM   #2
xyuf9002
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nice work!
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Old 04-26-2018, 08:11 AM   #3
F.Lazaro
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Nice. Thanks!
By the way, anyone has any experience with any of the S5 models?
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Old 05-01-2018, 01:33 PM   #4
seqsuave
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Thats interesting and really cool, thanks for that.
I didn't know the upgraded the S5, I wonder how the list prices compare to the S5 or S5 XL.

I have used S5 before, its a nice system I like it alot.
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Old 05-02-2018, 07:07 AM   #5
jhalpin
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We have an S5 that we're using 400bp chemistry on. It's been doing pretty well and is SO much easier to use than the PGM.

Can anyone comment on the 600bp kit? How is the size selection with it?

Last edited by jhalpin; 05-02-2018 at 07:09 AM.
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Old 05-03-2018, 08:06 AM   #6
keithsweatshirt
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The S5s are significantly easier to use and much less finicky than the PGMs. It's night and day. The Chef kits (400 bp) are pretty robust as are the ExT kits (600 bp).

The ExT kits take a lot less time than the Chef kits, 7 hours vs almost 13 or 14, I believe. Sequencing is also pretty quick at about 5 hours.

The 600 bp Chef ExT kits can do one chip at a time vs the 400 bp which are capable of doing two chips.
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Old 05-13-2018, 03:23 PM   #7
idedios
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I currently have an S5 and noticed after the January software update it was rebranded as the GeneStudio. The internals include a single Xeon E5-1650 v4, 128GB of DDR4 RAM, a GTX 1080, and a custom FPGA. It seems like S5 sequencers manufacturered at different times have different internals. It is also worth noting that the motherboard in the instrument is a dual-socket intel board with support for up to 512GB of RAM and multiple GPUs assuming you have a long enough PCIe riser cable for the FPGA. The built-in screen runs off the motherboard's integrated VGA graphics. TorrentSuite analysis is done with a VM that has access to 6 CPU cores and 40GB of RAM. Upgrading the internals is trivial and editing the QEMU config for the TSVM is also trivial however there is also the matter of changing the sun grid engine job scheduler config in the TSVM to use the additional cores.

The S5 XL by comparison is now branded the GeneStudio Prime and focuses on the additional compute of an external workstation as the Torrent Suite VM now runs natively on the external workstation. The S5 still needs to perform onboard analysis of the signal data via the FPGA otherwise it would take too long to transfer it over the 1Gb/s ethernet connection to the Torrent Suite workstation.
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Old 05-14-2018, 10:44 AM   #8
hutch08
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Checking out the Spec Sheets:
old S5's https://tinyurl.com/yc5zt5wu
new GeneStudio S5s: https://tinyurl.com/ya3vhdn2

You can compare the timing across the 540 chip to see that the Ion S5 and the Ion GeneStudio S5 share the same capability.

The Ion GeneStudio S5 Plus is slightly slower than the old Ion S5 XL, while the new Ion GeneStudio S5 Prime is slightly faster than the old Ion S5 XL.

Also worth noting that the new 550 chip that was introduced only runs on the GeneStudio S5 Plus, Prime or the old S5 XL...
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Old 07-10-2018, 11:44 AM   #9
r.rosati
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Quote:
Originally Posted by idedios View Post
I currently have an S5 and noticed after the January software update it was rebranded as the GeneStudio. The internals include a single Xeon E5-1650 v4, 128GB of DDR4 RAM, a GTX 1080, and a custom FPGA. It seems like S5 sequencers manufacturered at different times have different internals. It is also worth noting that the motherboard in the instrument is a dual-socket intel board with support for up to 512GB of RAM and multiple GPUs assuming you have a long enough PCIe riser cable for the FPGA. The built-in screen runs off the motherboard's integrated VGA graphics. TorrentSuite analysis is done with a VM that has access to 6 CPU cores and 40GB of RAM. Upgrading the internals is trivial and editing the QEMU config for the TSVM is also trivial however there is also the matter of changing the sun grid engine job scheduler config in the TSVM to use the additional cores.

The S5 XL by comparison is now branded the GeneStudio Prime and focuses on the additional compute of an external workstation as the Torrent Suite VM now runs natively on the external workstation. The S5 still needs to perform onboard analysis of the signal data via the FPGA otherwise it would take too long to transfer it over the 1Gb/s ethernet connection to the Torrent Suite workstation.
Hi,
did you upgrade your instrument in practice? I'd love to know details. I'm using an S5 now, but the processing times are indeed abysmal. It's taking 20 hours to process one chip (as opposed to the 16.5 hours suggested in the official folder) - and I'm not even including plugins.
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Old 07-12-2018, 10:56 AM   #10
r.rosati
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PS - in our S5, the VM has access to 12 cores. VM memory is indeed 40 GB.
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