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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 ge

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.

inciampati 8y ago
You can make your own reagents if you want to do sequencing reactions on this. It's not inconceivable. It's not necessary even to do sequencing. These systems are at their heart a general purpose microfluidic system, temperature controlled flowcell with high throughout fluorescence imaging capabilities. You can do a hell of a lot of stuff with that feature set.
braincode 8y ago
Good question! I've always wondered what would be required (in terms of equipment and raw materials) to make those reagents, I'm really curious to know how those get synthesized to and the level of purity/quality required for a successful sequencing run.
bayesian_horse 8y ago
I think the idea is to use these as "automatic microscopes" instead of as sequencers.
- jfmarkham 8y ago
  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.

inciampati 8y ago

You can make your own reagents if you want to do sequencing reactions on this. It's not inconceivable. It's not necessary even to do sequencing. These systems are at their heart a general purpose microfluidic system, temperature controlled flowcell with high throughout fluorescence imaging capabilities. You can do a hell of a lot of stuff with that feature set.

braincode 8y ago

Good question! I've always wondered what would be required (in terms of equipment and raw materials) to make those reagents, I'm really curious to know how those get synthesized to and the level of purity/quality required for a successful sequencing run.

bayesian_horse 8y ago

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

jfmarkham 8y ago
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.