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I just ran a couple of flowcells last week. I've ran 8 total so far now. My impression is that it can be very inconsistent depending on the quality of the flowc

I just ran a couple of flowcells last week. I've ran 8 total so far now. My impression is that it can be very inconsistent depending on the quality of the flowcell that they send you and your DNA prep. Great for smallish genomes (bacteria), not enough throughput/quality for large eukaryotic genomes (1gb+) unless you got money to burn.

oh_sigh 9y ago
$1,000 for the starter pack - what kind of use can you get out of that, and how much are the ongoing costs for the flowcells and anything else that needs to be replenished? Are you using it for fun? professionally? academically?
- aFLH7U2daj 9y ago
  Flow cells are 1000$ each (unless you buy a lot of them), the sequencer is basically a USB dongle with a uC in it and all the important stuff is in the flow cell. Flow cells are basically disposable (but you mail them back). You get one-ish use out of a flow cell though they can be "washed" and realoaded. Reagent kits run a few hundred dollars depending on what your doing and you get several uses out of them. IIRC it's not certified for use as a medical diagnostics device so it's "research only". It's a nice system with great (none) upfront costs that has a lot of potential. But read quality and quanity per dollar aren't as good as what we get with our NextSeq (which by contrast costs something crazy like 300-400k)
  - comstock 9y ago
    NextSeq is expensive, but there are cheaper options (from 30k) and you can just send your samples to a sequencing service. I’ve seen costs for a whole human genome at high coverage of between 1 and 3000USD.
    - chrisamiller 9y ago
      Be careful about defining "high coverage" as 30x. Many applications (especially cancer) really require 100x or more to overcome purity and ploidy, or to identify subclonal populations.
  - bayesian_horse 9y ago
    No sequencer on its own will ever be certified. You always need a pipeline from sample to a clinically useful answer to be certified. The problem here is that everything in that pipeline keeps improving at a fast base. Also the reference databases are updated all the time. Whereas sequencing will probably always give the right answer to the precise question it was given, I don't see any luck in certifying these methods any time soon.
- daemonk 9y ago
  I am using it professionally for a lab. The best bang for the buck right now is to buy their starter pack which includes library prep kit and 2 flow cells. This is limited to one per person. I got two members of the lab to buy two starter kits, effectively getting the flow cells for ~500 each. I am sure a lot of people are doing this too.
comstock 9y ago
It’s also comparatively expensive compared to other platforms (you can get a full human genome sequenced at high coverage for between 1000 and 3000 USD). The error rate is stupidly high (somewhere between 10 and 20%) compared to Illumina or Ion Torrent who give error rates far less than 1%. It can give very long reads, which are useful in some niche applications. But it’s been massively over-hyped (and over capitalized). The neat thing is that it’s very small. But that isn’t really compelling given the very low accuracy.
- eggie 9y ago
  > you can get a full human genome sequenced at high coverage for between 1000 and 3000 USD This is not a "full" human genome, but a collection of 150bp fragments that can be realigned to an existing human genome. You cannot take this and infer the whole diploid genome of the individual. There is a huge amount that will be missed, and all of our current knowledge is based on this gappy picture of what's going on in single genomes and human populations. > It can give very long reads, which are useful in some niche applications. But it’s been massively over-hyped (and over capitalized). I think you're dismissing the technology out of hand because of biases derived from much more limited short-read technology that only allows us to reliably see small variants <50bp. Without these long reads we can't see structural variation (SVs). There is an increasing amount of evidence that much of adaptive variation is driven by these kinds of variants. If you want recent evidence, see https://www.nature.com/articles/s41588-017-0010-y https://www.nature.com/articles/s41588-017-0010-y. There has long been evidence that there are huge copy number variations in humans, but these are still not evaluated reliably: http://science.sciencemag.org/content/330/6004/641 http://science.sciencemag.org/content/330/6004/641. We should be open to the possibility that our observational techniques are limiting our understanding how how genomes work. This has consistently occurred in the history of every observationally-driven science. It's amusing to me that people assume that SVs are "niche" when even the limited surveys of genomes we've been able to do with short reads show that roughly an equal number of base pairs in the human population vary due to small variants like SNPs and indels and big ones like deletions, insertions, and large scale copy number variation: http://science.sciencemag.org/content/330/6004/641 http://science.sciencemag.org/content/330/6004/641

oh_sigh 9y ago

$1,000 for the starter pack - what kind of use can you get out of that, and how much are the ongoing costs for the flowcells and anything else that needs to be replenished? Are you using it for fun? professionally? academically?

aFLH7U2daj 9y ago
Flow cells are 1000$ each (unless you buy a lot of them), the sequencer is basically a USB dongle with a uC in it and all the important stuff is in the flow cell. Flow cells are basically disposable (but you mail them back). You get one-ish use out of a flow cell though they can be "washed" and realoaded. Reagent kits run a few hundred dollars depending on what your doing and you get several uses out of them. IIRC it's not certified for use as a medical diagnostics device so it's "research only". It's a nice system with great (none) upfront costs that has a lot of potential. But read quality and quanity per dollar aren't as good as what we get with our NextSeq (which by contrast costs something crazy like 300-400k)
- comstock 9y ago
  NextSeq is expensive, but there are cheaper options (from 30k) and you can just send your samples to a sequencing service. I’ve seen costs for a whole human genome at high coverage of between 1 and 3000USD.
  - chrisamiller 9y ago
    Be careful about defining "high coverage" as 30x. Many applications (especially cancer) really require 100x or more to overcome purity and ploidy, or to identify subclonal populations.
- bayesian_horse 9y ago
  No sequencer on its own will ever be certified. You always need a pipeline from sample to a clinically useful answer to be certified. The problem here is that everything in that pipeline keeps improving at a fast base. Also the reference databases are updated all the time. Whereas sequencing will probably always give the right answer to the precise question it was given, I don't see any luck in certifying these methods any time soon.
daemonk 9y ago
I am using it professionally for a lab. The best bang for the buck right now is to buy their starter pack which includes library prep kit and 2 flow cells. This is limited to one per person. I got two members of the lab to buy two starter kits, effectively getting the flow cells for ~500 each. I am sure a lot of people are doing this too.

comstock 9y ago

It’s also comparatively expensive compared to other platforms (you can get a full human genome sequenced at high coverage for between 1000 and 3000 USD). The error rate is stupidly high (somewhere between 10 and 20%) compared to Illumina or Ion Torrent who give error rates far less than 1%. It can give very long reads, which are useful in some niche applications. But it’s been massively over-hyped (and over capitalized). The neat thing is that it’s very small. But that isn’t really compelling given the very low accuracy.

eggie 9y ago
> you can get a full human genome sequenced at high coverage for between 1000 and 3000 USD This is not a "full" human genome, but a collection of 150bp fragments that can be realigned to an existing human genome. You cannot take this and infer the whole diploid genome of the individual. There is a huge amount that will be missed, and all of our current knowledge is based on this gappy picture of what's going on in single genomes and human populations. > It can give very long reads, which are useful in some niche applications. But it’s been massively over-hyped (and over capitalized). I think you're dismissing the technology out of hand because of biases derived from much more limited short-read technology that only allows us to reliably see small variants <50bp. Without these long reads we can't see structural variation (SVs). There is an increasing amount of evidence that much of adaptive variation is driven by these kinds of variants. If you want recent evidence, see https://www.nature.com/articles/s41588-017-0010-y https://www.nature.com/articles/s41588-017-0010-y. There has long been evidence that there are huge copy number variations in humans, but these are still not evaluated reliably: http://science.sciencemag.org/content/330/6004/641 http://science.sciencemag.org/content/330/6004/641. We should be open to the possibility that our observational techniques are limiting our understanding how how genomes work. This has consistently occurred in the history of every observationally-driven science. It's amusing to me that people assume that SVs are "niche" when even the limited surveys of genomes we've been able to do with short reads show that roughly an equal number of base pairs in the human population vary due to small variants like SNPs and indels and big ones like deletions, insertions, and large scale copy number variation: http://science.sciencemag.org/content/330/6004/641 http://science.sciencemag.org/content/330/6004/641