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Oxford nanopore sequencing. If a few problems can be figured out (mainly around machine learning and protein design), then it will beat every other biological d

by koeng 6y ago

Oxford nanopore sequencing. If a few problems can be figured out (mainly around machine learning and protein design), then it will beat every other biological detection, diagnosis, and sequencing method by a massive amount (no 10x, but more like 100x-1000x) It's hard to explain how big nanopore sequencing is if a few (hard) kinks can be figured out. Basically, it has the potential to completely democratize DNA sequencing. Here is an explanation of the technology - https://www.youtube.com/watch?v=CGWZvHIi3i0 https://www.youtube.com/watch?v=CGWZvHIi3i0

dhash 6y ago
Best part is the Oxford devices are _actually affordable_. Illumina has had such a stranglehold on the market - devices start at around 35k and go up into “this is a house now” territory. Meanwhile the Flongle [0] is $99 and the main Oxford device can be had for $1k. [0] https://store.nanoporetech.com/us/flowcells/flongle-flow-cell.html https://store.nanoporetech.com/us/flowcells/flongle-flow-cel...
- bsder 6y ago
  > Illumina has had such a stranglehold on the market - devices start at around 35k and go up into “this is a house now” territory. You cannot effectively sell this kind of device under $25K--support costs simply eat your profit margin. This is a constant across industries. You either have a $250 thneed (and you ignore your customers) or a $25K thneed (and you have shitty customer support) or a $250K thneed (and you have decent customer support).
- zmmmmm 6y ago
  Depends what you mean by affordable - low barrier to entry, yes. But bases / $ is still orders of magnitude below where needed to displace Illumina for sequencing of large genomes (eg: human).
thewarrior 6y ago
Can this be used to make faster corona virus tests ? If so maybe this is the time to Manhattan project this technology.
- koeng 6y ago
  Generally, yes absolutely. I’ve been doing a project called “NanoSavSeq” (Nanopore Saliva Sequencing) in my free time. It’s published on dat right now since the raw files for Nanopore are really big (got too big for hashbase). There is one company doing it as well, but my version is completely open source and I’ve optimized it for affordable automation. To give you a sense, you can buy one for 1k and do as much detection as a 64k device, and it’s small enough to fit in a backpack. One device should be able to do 500-1000 tests per 24hrs at a cost of about $10 per test, not including labor.
  - iameoghan 6y ago
    Would love to know more. This is fascinating.
    - koeng 6y ago
      The dat website is at dat://aaca379867bff648f454337f36a65c8239f2437538f2a4e0b4b5eb389ea0caff You can visit with the beaker browser, or share it through dat so it won't ever go down. You can also visit it at http://www.nanosavseq.com/ http://www.nanosavseq.com/ (DNS is not up yet, http://167.172.195.83/book/index.html http://167.172.195.83/book/index.html is direct) It's embarrassingly barren right now, mainly since I've encountered some big problems with getting my DNA quantifier out of storage to start doing a lot more experiments. I'm getting that on Tuesday, so will be updating site then.
      - unixhero 6y ago
        The book / documentation is very clean and presented in a fantastic way. May I ask what engine you are using for presenting this book?
        koeng 6y ago
        mdbook! By the folks making the Rust docs. I love their formatting.
bionhoward 6y ago
Hell yes
deleted 6y ago
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by koeng 6y ago

dhash 6y ago

Best part is the Oxford devices are _actually affordable_. Illumina has had such a stranglehold on the market - devices start at around 35k and go up into “this is a house now” territory. Meanwhile the Flongle [0] is $99 and the main Oxford device can be had for $1k. [0] https://store.nanoporetech.com/us/flowcells/flongle-flow-cell.html https://store.nanoporetech.com/us/flowcells/flongle-flow-cel...

bsder 6y ago
> Illumina has had such a stranglehold on the market - devices start at around 35k and go up into “this is a house now” territory. You cannot effectively sell this kind of device under $25K--support costs simply eat your profit margin. This is a constant across industries. You either have a $250 thneed (and you ignore your customers) or a $25K thneed (and you have shitty customer support) or a $250K thneed (and you have decent customer support).
zmmmmm 6y ago
Depends what you mean by affordable - low barrier to entry, yes. But bases / $ is still orders of magnitude below where needed to displace Illumina for sequencing of large genomes (eg: human).

thewarrior 6y ago

Can this be used to make faster corona virus tests ? If so maybe this is the time to Manhattan project this technology.

koeng 6y ago
Generally, yes absolutely. I’ve been doing a project called “NanoSavSeq” (Nanopore Saliva Sequencing) in my free time. It’s published on dat right now since the raw files for Nanopore are really big (got too big for hashbase). There is one company doing it as well, but my version is completely open source and I’ve optimized it for affordable automation. To give you a sense, you can buy one for 1k and do as much detection as a 64k device, and it’s small enough to fit in a backpack. One device should be able to do 500-1000 tests per 24hrs at a cost of about $10 per test, not including labor.
- iameoghan 6y ago
  Would love to know more. This is fascinating.
  - koeng 6y ago
    The dat website is at dat://aaca379867bff648f454337f36a65c8239f2437538f2a4e0b4b5eb389ea0caff You can visit with the beaker browser, or share it through dat so it won't ever go down. You can also visit it at http://www.nanosavseq.com/ http://www.nanosavseq.com/ (DNS is not up yet, http://167.172.195.83/book/index.html http://167.172.195.83/book/index.html is direct) It's embarrassingly barren right now, mainly since I've encountered some big problems with getting my DNA quantifier out of storage to start doing a lot more experiments. I'm getting that on Tuesday, so will be updating site then.
    - unixhero 6y ago
      The book / documentation is very clean and presented in a fantastic way. May I ask what engine you are using for presenting this book?
      - koeng 6y ago
        mdbook! By the folks making the Rust docs. I love their formatting.

bionhoward 6y ago

Hell yes

deleted 6y ago

[deleted]