
ReSeq: Repurposing HiSeq DNA Sequencers - kasbah
https://reseq.hackteria.org/
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snarfy
Mikeselectricstuff has some teardown videos of DNA sequencers. Interesting
stuff.

[https://www.youtube.com/watch?v=XaumUp4GpCw](https://www.youtube.com/watch?v=XaumUp4GpCw)

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kasbah
I am part of this project but just about to board a 2 hour flight. If you have
any questions, feel free to post below and I will answer them later.

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ak217
This is very cool. I hope you get some cool uses out of this.

What's the max frame rate you can get out of the cameras (without tiling)? Are
you able to control focus and camera gain?

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kasbah
Thanks, working out the max frame rate is a bit complicated by the fact it
uses time delay integration (TDI) scanning. There are 4 TDI cameras each 2048
* 128 pixels. I couldn't find any official documentation (the cameras are
Hamamatsu S10405 CCDs and there is one C10000-509 control board for 2 cameras
each). I think it's the same sensor as this camera which quotes the line rate
at 50khz.
[https://www.hamamatsu.com/resources/pdf/sys/SCAS0085E_C10000...](https://www.hamamatsu.com/resources/pdf/sys/SCAS0085E_C10000-801.pdf)

This Ebay listing quotes the line rate as 1khz, not sure where they got that:
[https://www.ebay.com/itm/4-Illumina-
HiSeq-2000-Hamamatsu-S10...](https://www.ebay.com/itm/4-Illumina-
HiSeq-2000-Hamamatsu-S10405-Line-CCD-Camera-/372264830253)

We were able to grab a live video feed from a single camera, that must have
been 20fps at least, but we'll have to investigate fully.

Yes, we are able adjust the gain and are able to focus both by moving the
stage and by adjusting the more fine-grained piezo focus actuator (but we'd
like to be able auto-focus using Micro Manager: [https://micro-
manager.org](https://micro-manager.org)).

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ak217
Nice. I suspect there are quite a few Illumina engineers secretly cheering for
you.

I'm in touch with a community of microscopy folks which includes the
maintainers of Micro Manager. I'll send this link around, I bet they'll be
interested.

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astazangasta
What about reagents? The sequencers themselves are expensive, but library kits
cost a lot of money, as do the reagents for running a flow cell. Even if I can
get a sequencer for free, if I still have to pay through the nose for reagents
it's no good. Especially as these sequencers become obsolete and people stop
MAKING the relevant reagents, and their cost goes higher and higher.

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bayesian_horse
I think the idea is to use these as "automatic microscopes" instead of as
sequencers.

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jfmarkham
I'm also involved in the project. Ideally we'd like it to be able to be used
both as both a microscope and as a sequencer. Potentially there are other uses
too. For example this paper uses a customised Illumina GAIIx sequencer to do
high throughput measurement of on and off rates:
[https://www.pnas.org/content/114/21/5461](https://www.pnas.org/content/114/21/5461)
While this does involve sequencing with Illumina reagents, my point is that
it's possible to use customised flow cells and reagents for new assays that
you might dream up. Software to run such assays could be built on top of what
we are doing.

I have heard that the BGISEQ-500 ([https://www.bgi.com/resources/sequencing-
platforms](https://www.bgi.com/resources/sequencing-platforms)) is a similar
machine...

Our initial focus is on writing the device adapters that enable Micro-Manager
([https://micro-manager.org](https://micro-manager.org)) to talk to the HiSeq
hardware. MM will then be able to drive it like a microscope as well as
providing access to all the other fluidics switches, pumps, sensors etc. The
MM user interface is extensible and plugins can be written to support assays
such as sequencing. MM also exposes all of the devices and functionality in a
scripting environment.

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adenadel
Here's another series of posts where they tear down one of the original
Illumina sequencers (the Genome Analyzer).

[https://blogs.swarthmore.edu/Illumina+GAIIx+Teardown/](https://blogs.swarthmore.edu/Illumina+GAIIx+Teardown/)

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skosuri
Ooh. I got a HiSeq 2000 for a six pack of beer. Can’t wait to try to hack it!

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kasbah
You should become an alpha tester!

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subcosmos
I just nabbed a cheap one as well. Happy to join the community.

Question for you though: it appears to be just an inch too big to fit into my
building. How difficult is it to split into manageable chunks. Do the 4
modules separate without too much hassle, or are we talking full teardown?

~~~
kasbah
It's pretty modular. Urs Gaudenz removed the fluidic pump and fridge on his to
reduce the size.

~~~
subcosmos
Where's the best place to chat with the community? Got a slack channel or
anything?

~~~
kasbah
In the forum currently: [https://forum.hackteria.org/t/hiseq2000-next-level-
hacking/3...](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325)

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hyperbovine
Boy, do I feel old. HiSeq 2500 was a gold-standard, $750k machine when I was
starting grad school. Which was not that long ago, or so I thought.

