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A used laboratory grade NGS system can be had for less than 10K https://www.ebay.com/itm/265148387179 https://www.ebay.com/itm/265148387179 Nanopore is still

A used laboratory grade NGS system can be had for less than 10K https://www.ebay.com/itm/265148387179 https://www.ebay.com/itm/265148387179 Nanopore is still not quite ready yet for precise and high accuracy sequencing. Give it another five years.

mylons 5y ago
wow i didn’t know they were that “cheap” now. i used to work for a major competitor to the sequencer you linked, the SOLiD. and i feel like nanopore is the VR of dna sequencing. it’s always just another few years off.
- joshuamcginnis 5y ago
  What do you mean by it's always a few years off? Nanopore will allow you to do high-quality genomic sequencing _now_, in a home lab if you wanted, for less than $3K. If you amortize the 3K by the number of genomes you can sequence on the same flow cell, the price per base or per genome falls precipitously, depending on the size of the genome of course.
- ampdepolymerase 5y ago
  The one I linked to is a decade out of date and OEM discontinued.
  - mylons 5y ago
    ya my first thought was how hard are reagents to get, but probably not that hard. i wasn’t in the lab, i was in bioinformatics so i’m generally clueless on reagent acquisition.
- divbzero 5y ago
  > and i feel like nanopore is the VR of dna sequencing. it’s always just another few years off. Is this also true for nanopores in protein sequencing? This HN comment from a few weeks back [1] pointed out recent progress but perhaps the tech is still not quite there. [1]: https://news.ycombinator.com/item?id=29481075 https://news.ycombinator.com/item?id=29481075
- haihaibye 5y ago
  Occulus sold 8.1m units this year, more than XBox.
AstroDogCatcher 5y ago
Interested outsider here; I work with a lot of HCLS research customers but don't have a biology-related background. Can you explain the problems with the Nanopore sequencer accuracy in more detail? Basically, I was wondering if I could get one for myself and sequence my own genome, then user the data to learn about life-sciences computing techniques. If I were to buy one of the USB-attachable devices and run it, is the data simply not viable for use in a genomics pipeline, or is it just that the results would be questionable? Also, if accuracy is an issue, what about just running the same sample N times and doing some error correction?
- ampdepolymerase 5y ago
  I recommend reading this review https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1935-5 https://genomebiology.biomedcentral.com/articles/10.1186/s13... I guess there are limits to ensemble methods if the underlying accuracy doesn't increase. I don't work on gene sequencing algorithms but from what I understand of ML ensemble techniques, there are certain assumptions regarding the underlying independence of the errors. The errors for nanopore should be uniform but I am not sure. Any molecular biologist here care to comment?
  - biophysboy 5y ago
    I know that the error rate of the oxford nanopore sequencer depends on GC content (guanine/cytosine nucleotides), and that the Pacific Biosciences sequencer uses a polymerase that gets worn down during reading. So there is some non-uniformity in the chemistry.
    - ampdepolymerase 5y ago
      GC rich regions as in hairpin loops? How would the sequencer deal with those?
      - biophysboy 5y ago
        If I'm not mistaken the nanopore tech unwinds double-stranded DNA during the reading, so I don't think hairpins are the issue.
anderspitman 5y ago
I work in a dry lab but I'm pretty sure you need a lot of expensive chemicals to actually make one of these work, yeah?
- mylons 5y ago
  yup. that’s the business model for Illumina. it’s very much akin to video game consoles. Illumina might take a hit on selling the machine but makes it up in selling you proprietary reagents.
rbartelme 5y ago
Cost/benefit analysis may dictate that, as other posters suggested, you'd be better served to get raw fastq files from a sequencing lab. Even better if you can send the lab a sample and they'll process the extractions for extra $$.
joshuamcginnis 5y ago
That's not true. I just did a high-quality sequence and assembly of a new species of fungus from my home lab using nanopore. You can see all my code used for assembly and analysis that will be referenced in a paper I plan to publish in Jan here: https://github.com/EverymanBio/pestalotiopsis https://github.com/EverymanBio/pestalotiopsis
- pas 5y ago
  How do you know the quality of the resulting sequence?
  - ampdepolymerase 5y ago
    You don't, not without either resequencing it with another sequencing system or benchmarking the sequencer with a known sequence.
  - deleted 5y ago
    [deleted]
  - joshuamcginnis 5y ago
    There are quality checks throughout the entire process, starting from the raw read quality scores returned directly from the sequencer all the way to fully assembled genome completeness. In our paper, one of the tools we used for this is called BUSCO[0] which scored our assembly at 97.9%, a relatively high score for de novo assemblies. [0] https://pubmed.ncbi.nlm.nih.gov/31020564/ https://pubmed.ncbi.nlm.nih.gov/31020564/
- lawrenceyan 5y ago
  Given that the decoder is machine-learned and depends on a training set to go from squiggle -> ATGC..., how do you ensure that sequences which haven't been seen before (not in the training set) are still accurately accounted for?
  - joshuamcginnis 5y ago
    We used Guppy for basecalling, which is neural network based and used to turn raw signal data into the predicted bases. There're no guarantees of accuracy, only tools to determine and assess quality. One major way of assessing accuracy is to compare the subject genome with other similar reference genomes and denote the high-degree of homology in highly-conserved regions.
rootsudo 5y ago
What sort of books/videos do you suggest so one can learn more? This stuff is interesting, and I've always seen inexpensive lab equipment on ebay. If this can sequence flora, fungi and human DNA for about 10k - I'd buy it, just to experiment and deep dive. That is such a low barrier of entry it itself is interesting.

mylons 5y ago

wow i didn’t know they were that “cheap” now. i used to work for a major competitor to the sequencer you linked, the SOLiD. and i feel like nanopore is the VR of dna sequencing. it’s always just another few years off.

joshuamcginnis 5y ago
What do you mean by it's always a few years off? Nanopore will allow you to do high-quality genomic sequencing _now_, in a home lab if you wanted, for less than $3K. If you amortize the 3K by the number of genomes you can sequence on the same flow cell, the price per base or per genome falls precipitously, depending on the size of the genome of course.
ampdepolymerase 5y ago
The one I linked to is a decade out of date and OEM discontinued.
- mylons 5y ago
  ya my first thought was how hard are reagents to get, but probably not that hard. i wasn’t in the lab, i was in bioinformatics so i’m generally clueless on reagent acquisition.
divbzero 5y ago
> and i feel like nanopore is the VR of dna sequencing. it’s always just another few years off. Is this also true for nanopores in protein sequencing? This HN comment from a few weeks back [1] pointed out recent progress but perhaps the tech is still not quite there. [1]: https://news.ycombinator.com/item?id=29481075 https://news.ycombinator.com/item?id=29481075
haihaibye 5y ago
Occulus sold 8.1m units this year, more than XBox.

AstroDogCatcher 5y ago

Interested outsider here; I work with a lot of HCLS research customers but don't have a biology-related background. Can you explain the problems with the Nanopore sequencer accuracy in more detail? Basically, I was wondering if I could get one for myself and sequence my own genome, then user the data to learn about life-sciences computing techniques. If I were to buy one of the USB-attachable devices and run it, is the data simply not viable for use in a genomics pipeline, or is it just that the results would be questionable? Also, if accuracy is an issue, what about just running the same sample N times and doing some error correction?

ampdepolymerase 5y ago
I recommend reading this review https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1935-5 https://genomebiology.biomedcentral.com/articles/10.1186/s13... I guess there are limits to ensemble methods if the underlying accuracy doesn't increase. I don't work on gene sequencing algorithms but from what I understand of ML ensemble techniques, there are certain assumptions regarding the underlying independence of the errors. The errors for nanopore should be uniform but I am not sure. Any molecular biologist here care to comment?
- biophysboy 5y ago
  I know that the error rate of the oxford nanopore sequencer depends on GC content (guanine/cytosine nucleotides), and that the Pacific Biosciences sequencer uses a polymerase that gets worn down during reading. So there is some non-uniformity in the chemistry.
  - ampdepolymerase 5y ago
    GC rich regions as in hairpin loops? How would the sequencer deal with those?
    - biophysboy 5y ago
      If I'm not mistaken the nanopore tech unwinds double-stranded DNA during the reading, so I don't think hairpins are the issue.

anderspitman 5y ago

I work in a dry lab but I'm pretty sure you need a lot of expensive chemicals to actually make one of these work, yeah?

mylons 5y ago
yup. that’s the business model for Illumina. it’s very much akin to video game consoles. Illumina might take a hit on selling the machine but makes it up in selling you proprietary reagents.

rbartelme 5y ago

Cost/benefit analysis may dictate that, as other posters suggested, you'd be better served to get raw fastq files from a sequencing lab. Even better if you can send the lab a sample and they'll process the extractions for extra $$.

joshuamcginnis 5y ago

That's not true. I just did a high-quality sequence and assembly of a new species of fungus from my home lab using nanopore. You can see all my code used for assembly and analysis that will be referenced in a paper I plan to publish in Jan here: https://github.com/EverymanBio/pestalotiopsis https://github.com/EverymanBio/pestalotiopsis

pas 5y ago
How do you know the quality of the resulting sequence?
- ampdepolymerase 5y ago
  You don't, not without either resequencing it with another sequencing system or benchmarking the sequencer with a known sequence.
- deleted 5y ago
  [deleted]
- joshuamcginnis 5y ago
  There are quality checks throughout the entire process, starting from the raw read quality scores returned directly from the sequencer all the way to fully assembled genome completeness. In our paper, one of the tools we used for this is called BUSCO[0] which scored our assembly at 97.9%, a relatively high score for de novo assemblies. [0] https://pubmed.ncbi.nlm.nih.gov/31020564/ https://pubmed.ncbi.nlm.nih.gov/31020564/
lawrenceyan 5y ago
Given that the decoder is machine-learned and depends on a training set to go from squiggle -> ATGC..., how do you ensure that sequences which haven't been seen before (not in the training set) are still accurately accounted for?
- joshuamcginnis 5y ago
  We used Guppy for basecalling, which is neural network based and used to turn raw signal data into the predicted bases. There're no guarantees of accuracy, only tools to determine and assess quality. One major way of assessing accuracy is to compare the subject genome with other similar reference genomes and denote the high-degree of homology in highly-conserved regions.

rootsudo 5y ago

What sort of books/videos do you suggest so one can learn more? This stuff is interesting, and I've always seen inexpensive lab equipment on ebay. If this can sequence flora, fungi and human DNA for about 10k - I'd buy it, just to experiment and deep dive. That is such a low barrier of entry it itself is interesting.