4 ms·

We are not “in the nanopore era of sequencing”. We are (still) firmly in the sequencing by synthesis era. Yes it requires chopping the genome opening small(er)

We are not “in the nanopore era of sequencing”. We are (still) firmly in the sequencing by synthesis era. Yes it requires chopping the genome opening small(er) pieces (than with Nanopore sequencing) and then reconstructing the genome based on a reference (and this has its issues). But Nanopore sequencing is still far from perfect due to its high error rate. Any clinical sequencing is still done using sequencing by synthesis (at which Illumina has gotten very good over the past decade). Nanopore devices are truly cool, small and comparatively cheap though, and you can compensate for the error rate by just sequence everything multiple times. I’m not too familiar with the economics of this approach though. With sbs technology you could probably sequence your whole genome 30 times (a normal “coverage”) for below 1000€/$ with a reputable company. I’ve seen 180$, but not sure if I’d trust that.

Danjoe4 1y ago
Nanopore is good for hybrid sequencing. You can align the higher quality illumina reads against its longer contiguous reads
Metacelsus 1y ago
>you can compensate for the error rate by just sequence everything multiple times. Usually, but sometimes the errors are correlated. Overall I agree, short read sequencing is a lot more cost effective. Doing an Illumina whole genome sequence for cell line quality control (at my startup) costs $260 in total.
bonsai_spool 1y ago
> But Nanopore sequencing is still far from perfect due to its high error rate. Any clinical sequencing is still done using sequencing by synthesis (at which Illumina has gotten very good over the past decade). There is no reason for Nanopore to supplant sequencing-by-synthesis for short reads - that's largely solved and getting cheaper all the while. The future clinical utility will be in medium- and large-scale variation. We don't understand this in the clinical setting nearly as well as we understand SNPs. So Nanopore is being used in the research setting and to diagnose individuals with very rare genetic disorders. (edit) > We are not “in the nanopore era of sequencing”. We are (still) firmly in the sequencing by synthesis era. I also strongly disagree. SBS is very reliable but it's common (if Toyota is the most popular car, does that mean we're in the Toyota internal combustion era? Or can Waymo still matter despite its small footprint?). Novelty in sequencing is coming from ML approaches, RNA-DNA analysis, and combining long- and short-read technologies.
- teekert 1y ago
  I agree with you. Long reads lead to new insights and over time to better diagnoses by providing better understanding of large(r) scale aberrations, and as the tech gets better will be able to do so more easily. But is really not there yet. It’s mostly research and somehow it’s not really improving as much as hoped, I get the feeling.
Onavo 1y ago
You can get it pretty damn cheap if you are willing to send your biological data overseas. Nebula genomics and a lot of other biotechs do this by essentially outsourcing to China. There's no particular technology secret, just cheaper labor and materials.
- vintermann 1y ago
  Can you trust it though? It'd be trivially easy to do a 1x read, maybe 2x, and then fake the other 28 reads. And it'd be hard to catch someone doing this without doing another 30x read from someone you trust. There's famously a lot of cheating in medical research, it would be odd if everyone stopped the moment they left academia (there have been scandals with forensic labs cheating too, now that I think about it).
- gillesjacobs 1y ago
  They save money by cheap labour and batching large quantities for analysis. For the consumer this means long wait times and potentially expired DNA samples. I tried two samples with Nebula, waited 11 months total. Both samples failed. Got a refund on the service but spent 50usd in postage for the sample kit.
- deleted 1y ago
  [deleted]
BobbyTables2 1y ago
I’ve always wondered how the reconstruction works. It would be difficult to break a modest program into basic blocks and then reconstruct it. Same with paragraphs in a book. How does this work with DNA?
- bonsai_spool 1y ago
  This is very easily googled. There are new algorithmic advances for new kinds of sequencing data but this is the key (from the 70s) https://en.wikipedia.org/wiki/Burrows–Wheeler_transform https://en.wikipedia.org/wiki/Burrows–Wheeler_transform
- vintermann 1y ago
  They exploit the fact that so much of our DNA is the same. They basically have the book with no typos, or rather with only the typos they've decided to call canonical. So given a short sentence excerpt, even with a few errors thrown in, partial string matching is usually able to figure out where in the book it was likely from. Sometimes there may be more possibilities, but then you can look at overlaps and count how many times a particular variant appears in one context vs. another. One problem is, DNA contains a lot of copies and repetitive stretches, as if the book had "all work and no play makes jack a dull boy" repeated end to end for a couple of pages. Then it can hard to place where the variant actually is. Longer reads helps with this.
- jakobnissen 1y ago
  There are two ways: Assembly by mapping and de Novo assembly. If you already have a human genome file, you can take each DNA piece and map it to its closest match in the genome. If you can cover the whole genome this way, you are done. The alternative way is to exploit overlaps between DNA fragments. If two 1000 bp pieces overlap with 900 basepairs, that's probably because they come from two 1000 regions of your genome that overlap by 900 baswpairs. You can then merge the pieces. By iteratively merging millions of fragments you can reconstruct the original genome. Both these approaches are surprisingly and delightfully deep computational problems that have been researched for decades.
- __MatrixMan__ 1y ago
celltalk 1y ago
This is wrong, a lot of diagnostic labs are actually going for nanopore sequencing since its prep is overall cheaper compared to alternatives. Also the sensitivity for related regions are usually matching qPCR, and it can give you more information such as methylation on top of that. A recent paper on classifying acute leukemia via nanopore: https://www.nature.com/articles/s41588-025-02321-z/figures/8 https://www.nature.com/articles/s41588-025-02321-z/figures/8 The timelines are exaggarated but still it works and that’s what matters in diagnostics.
jefftk 1y ago
> We are (still) firmly in the sequencing by synthesis era. It really depends what your goals are. At the NAO we use Illumina with their biggest flow cell (25B) for wastewater because the things we're looking for (ex: respiratory viruses) are a small fraction of the total nucleic acids and we need the lowest cost per base pair. But when we sequence nasal swabs these viruses are a much higher fraction, and the longer reads and lower cost per run of Nanopore make it a better fit.
the__alchemist 1y ago
I guess this depends on the applciation. For whole human genome? Not nanopore era. For plasmids? Absolutely. I'm a nobody, and I can drop a tube into a box in a local university, and get the results emailed to me by next morning for $15USD. This is due to a streamlined nanopore-based workflow.

Danjoe4 1y ago

Nanopore is good for hybrid sequencing. You can align the higher quality illumina reads against its longer contiguous reads

Metacelsus 1y ago

>you can compensate for the error rate by just sequence everything multiple times. Usually, but sometimes the errors are correlated. Overall I agree, short read sequencing is a lot more cost effective. Doing an Illumina whole genome sequence for cell line quality control (at my startup) costs $260 in total.

bonsai_spool 1y ago

> But Nanopore sequencing is still far from perfect due to its high error rate. Any clinical sequencing is still done using sequencing by synthesis (at which Illumina has gotten very good over the past decade). There is no reason for Nanopore to supplant sequencing-by-synthesis for short reads - that's largely solved and getting cheaper all the while. The future clinical utility will be in medium- and large-scale variation. We don't understand this in the clinical setting nearly as well as we understand SNPs. So Nanopore is being used in the research setting and to diagnose individuals with very rare genetic disorders. (edit) > We are not “in the nanopore era of sequencing”. We are (still) firmly in the sequencing by synthesis era. I also strongly disagree. SBS is very reliable but it's common (if Toyota is the most popular car, does that mean we're in the Toyota internal combustion era? Or can Waymo still matter despite its small footprint?). Novelty in sequencing is coming from ML approaches, RNA-DNA analysis, and combining long- and short-read technologies.

teekert 1y ago
I agree with you. Long reads lead to new insights and over time to better diagnoses by providing better understanding of large(r) scale aberrations, and as the tech gets better will be able to do so more easily. But is really not there yet. It’s mostly research and somehow it’s not really improving as much as hoped, I get the feeling.

Onavo 1y ago

You can get it pretty damn cheap if you are willing to send your biological data overseas. Nebula genomics and a lot of other biotechs do this by essentially outsourcing to China. There's no particular technology secret, just cheaper labor and materials.

vintermann 1y ago
Can you trust it though? It'd be trivially easy to do a 1x read, maybe 2x, and then fake the other 28 reads. And it'd be hard to catch someone doing this without doing another 30x read from someone you trust. There's famously a lot of cheating in medical research, it would be odd if everyone stopped the moment they left academia (there have been scandals with forensic labs cheating too, now that I think about it).
gillesjacobs 1y ago
They save money by cheap labour and batching large quantities for analysis. For the consumer this means long wait times and potentially expired DNA samples. I tried two samples with Nebula, waited 11 months total. Both samples failed. Got a refund on the service but spent 50usd in postage for the sample kit.
deleted 1y ago
[deleted]

BobbyTables2 1y ago

I’ve always wondered how the reconstruction works. It would be difficult to break a modest program into basic blocks and then reconstruct it. Same with paragraphs in a book. How does this work with DNA?

bonsai_spool 1y ago
This is very easily googled. There are new algorithmic advances for new kinds of sequencing data but this is the key (from the 70s) https://en.wikipedia.org/wiki/Burrows–Wheeler_transform https://en.wikipedia.org/wiki/Burrows–Wheeler_transform
vintermann 1y ago
They exploit the fact that so much of our DNA is the same. They basically have the book with no typos, or rather with only the typos they've decided to call canonical. So given a short sentence excerpt, even with a few errors thrown in, partial string matching is usually able to figure out where in the book it was likely from. Sometimes there may be more possibilities, but then you can look at overlaps and count how many times a particular variant appears in one context vs. another. One problem is, DNA contains a lot of copies and repetitive stretches, as if the book had "all work and no play makes jack a dull boy" repeated end to end for a couple of pages. Then it can hard to place where the variant actually is. Longer reads helps with this.
jakobnissen 1y ago
There are two ways: Assembly by mapping and de Novo assembly. If you already have a human genome file, you can take each DNA piece and map it to its closest match in the genome. If you can cover the whole genome this way, you are done. The alternative way is to exploit overlaps between DNA fragments. If two 1000 bp pieces overlap with 900 basepairs, that's probably because they come from two 1000 regions of your genome that overlap by 900 baswpairs. You can then merge the pieces. By iteratively merging millions of fragments you can reconstruct the original genome. Both these approaches are surprisingly and delightfully deep computational problems that have been researched for decades.
__MatrixMan__ 1y ago

celltalk 1y ago

This is wrong, a lot of diagnostic labs are actually going for nanopore sequencing since its prep is overall cheaper compared to alternatives. Also the sensitivity for related regions are usually matching qPCR, and it can give you more information such as methylation on top of that. A recent paper on classifying acute leukemia via nanopore: https://www.nature.com/articles/s41588-025-02321-z/figures/8 https://www.nature.com/articles/s41588-025-02321-z/figures/8 The timelines are exaggarated but still it works and that’s what matters in diagnostics.

jefftk 1y ago

> We are (still) firmly in the sequencing by synthesis era. It really depends what your goals are. At the NAO we use Illumina with their biggest flow cell (25B) for wastewater because the things we're looking for (ex: respiratory viruses) are a small fraction of the total nucleic acids and we need the lowest cost per base pair. But when we sequence nasal swabs these viruses are a much higher fraction, and the longer reads and lower cost per run of Nanopore make it a better fit.

the__alchemist 1y ago

I guess this depends on the applciation. For whole human genome? Not nanopore era. For plasmids? Absolutely. I'm a nobody, and I can drop a tube into a box in a local university, and get the results emailed to me by next morning for $15USD. This is due to a streamlined nanopore-based workflow.