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Old 12-07-2016, 08:52 AM   #1
Erwin
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Default feedback from PromethION users

Dear fellow sequencers,

We are in the process of acquiring a PromethION instrument and I wondered if there is already some feedback on its use. If there is anyone who has a PromethION in the lab and has done some runs on it I'd be eager to know.

Best wishes and thanks in advance
Erwin
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Old 12-07-2016, 09:04 AM   #2
GenoMax
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I don't have an answer for your question but you may find this recent blog post about PromethION from Dr. Keith Robinson interesting.
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Old 12-07-2016, 02:31 PM   #3
wdecoster
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I don't think there are already customers who generated (a lot of) data. There is a bit of a delay with deliveries of sequencers and/or flowcells. I don't really agree with the blog post of Keith Robinson (linked by GenoMax) and think PromethION will be an important (r)evolution in genome sequencing.
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Old 12-07-2016, 05:06 PM   #4
Brian Bushnell
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There are some major logistical hurdles for PromethION. I found out yesterday that we are getting one, and it needs 2 dedicated 10 gigabit Ethernet links. If you want to store the data so as to be able to re-call it later, that could fill (based on those specs) over 40 4TB HDDs per day. I doubt we have the capacity to transfer to tape at that speed.
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Old 12-08-2016, 01:02 AM   #5
wdecoster
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It's pretty much a data monster and we also need to think how to cope with that. But at this rate, it won't take too long that long term storing data gets more expensive than just generating the sequence again when you need it, given that the sample isn't rare.
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Old 12-08-2016, 04:30 AM   #6
GenoMax
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The devil is always in the details.

Let us say PromethION does work "as advertised", it certainly is not going to be for a lab group or even some cores. You would need to have the necessary infrastructure (and proven demand to boot) to fully utilize capacity of a beast like this. Not keeping these monster machines running 24x7 inevitably leads to "issues".
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Old 12-19-2016, 01:56 PM   #7
wdecoster
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Quote:
Originally Posted by GenoMax View Post
You would need to have the necessary infrastructure (and proven demand to boot) to fully utilize capacity of a beast like this. Not keeping these monster machines running 24x7 inevitably leads to "issues".
(Having thought more about this... while preparing for our PromethION...)
There is no discussion that you'll indeed need a pretty extensive (storage and compute) infrastructure. But I'm not sure that running 24/7 is as required as you suggest. What would be the reason for the need to run 24/7?

The machine is quite modular. You can run everything between 1 and 48 flow cells, depending on demand.
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Old 12-19-2016, 05:16 PM   #8
GenoMax
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Quote:
Originally Posted by wdecoster View Post
(Having thought more about this... while preparing for our PromethION...)
There is no discussion that you'll indeed need a pretty extensive (storage and compute) infrastructure. But I'm not sure that running 24/7 is as required as you suggest. What would be the reason for the need to run 24/7?

The machine is quite modular. You can run everything between 1 and 48 flow cells, depending on demand.
Let me say this first. You are rightfully excited about this technology and are sold on it promise. If the technology indeed works as advertised then you should have no worries.

Having worked with many new sequencers over the years I tend to err on side of caution, when it comes to brand new sequencers. Current sequencers are a marvel of chemistry, nanotechnology, engineering and contain many precision manufactured parts that need to absolutely work 100% (or close to) for the sequencing magic to happen. There are pumps, small capillaries, manifolds, solenoid valves, electrical sensors that can be easily foiled by an air bubble, a small salt crystal, a spec of dust, you get the idea. For this reason, Illumina's recommendation is to wash sequencers regularly, even if one is not using them. I have seen examples of PacBio RSII sequencers working well when they are used regularly as opposed to ones that are not.

Even though PromethION is modular one would want to ensure that one will be using all spots for flowcells. And to do that there needs to be enough ongoing demand. (Note: Don't count on the pent-up demand during the first quarter since many would be waiting to get their hands on this tech but think about six months+ out).

I think you don't work on the bench experiment side of things? People are sometimes blindsided by how quickly reagent costs add up when sequencers are run regularly. It is not uncommon for core labs to run up annual tabs in the millions of dollars just for reagents.

PromethION tech may prove resilient/robust and we will know for sure in the first year. It will certainly be essential for its market success.

It would be interesting to hear how things fare (not on informatics side but on experimental bench side) once you get your PromethION going.
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Old 12-20-2016, 12:47 AM   #9
wdecoster
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Quote:
Originally Posted by GenoMax View Post
Having worked with many new sequencers over the years I tend to err on side of caution, when it comes to brand new sequencers. Current sequencers are a marvel of chemistry, nanotechnology, engineering and contain many precision manufactured parts that need to absolutely work 100% (or close to) for the sequencing magic to happen. There are pumps, small capillaries, manifolds, solenoid valves, electrical sensors that can be easily foiled by an air bubble, a small salt crystal, a spec of dust, you get the idea. For this reason, Illumina's recommendation is to wash sequencers regularly, even if one is not using them. I have seen examples of PacBio RSII sequencers working well when they are used regularly as opposed to ones that are not.

Even though PromethION is modular one would want to ensure that one will be using all spots for flowcells. And to do that there needs to be enough ongoing demand. (Note: Don't count on the pent-up demand during the first quarter since many would be waiting to get their hands on this tech but think about six months+ out).
Thanks for the clarification.

Quote:
Originally Posted by GenoMax View Post
I think you don't work on the bench experiment side of things?
Unfortunately, I'm a hybrid PhD student splitting my time between 90% in the wet lab and 90% behind my pc. I have a preference for the in silico work and I pretty much suck in the lab. I've been told by my colleagues that I'm not allowed to touch the PromethION ;-)

Quote:
Originally Posted by GenoMax View Post
It would be interesting to hear how things fare (not on informatics side but on experimental bench side) once you get your PromethION going.
It will take a few months before things are up and running, but I'll let you know.
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