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Nanopore MinION – $1k solid-state DNA sequencers

nanoporetech.com

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Re: Nanopore MinION – $1k solid-state DNA sequencers

#61

Post by eggie »

zmmmmm wrote: post #59
eggie wrote: post #51

Earlier quoted context omitted.

> 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 si…

I think you are not sufficiently recognising how much structural variation can be resolved from short reads. There is certainly some that can't but a large proportion can be with the right tools.

I've participated in several large projects that worked to detect SVs from short reads in humans. The results, which remain best of class, are simply disappointing. A tiny fraction of the variants detected were actually resolvable to near-base pair resolution. The vast majority were described in approximate terms, using estimates of breakpoints and allelic structure.

Most structural variation I've seen based on whole genome assemblies is not even classifiable into neat categories like "deletion" or "insertion". If you think that "most" things are detected with short reads then you are deluded by the dominant technology.

Re: Nanopore MinION – $1k solid-state DNA sequencers

#62

Post by eggie »

comstock wrote: post #53
eggie wrote: post #51

Earlier quoted context omitted.

> 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 si…

I’d agree with you, that long reads would be useful if the error rate wasn’t so shockingly bad. There is, likely value in long reads, but what non-niche research applications are there for highly error’d reads that justify a valuation of several billion dollars?

The per base error rate is bad. In the case of pacbio, this error process approximates white noise, and so you can deal with it perfectly by increasing read coverage. Things are somewhat complicated with the nanopore tech described in this post, as errors may be correlated due to the way the basecalling is done, but in practice it's nearly as big a problem as you think it is.

For things approaching a read length the per-base error rate of a single read is simply irrelevant. In practice, with sufficient coverage (e.g. 20x) you simply don't care about the per base error rate of the reads.

Re: Nanopore MinION – $1k solid-state DNA sequencers

#63

Post by eggie »

sdcuevas wrote: post #54

Oxford Nanopore is burning through at least $1 million a week of their investors income with virtually no sales to support their market valuation. Will they be the next Theranos? https://www.jcapitalresearch.com/uploads/2/0/0/3/20032477/20...

The technology really works and is generating results at a rapid pace. This will absolutely not be the next Theranos, although you may be right that there are issues of burnrate and maybe even mismanagement.

To me the fact that they have a patent monopoly on "putting DNA through a protein pore with voltage sensing" is tragic. Who knows were we would be today if these patents had been granted to the public domain.

Re: Nanopore MinION – $1k solid-state DNA sequencers

#64

Post by eggie »

callesgg wrote: post #27
bmcusick wrote: post #3

So what’s a whole human genome sequence cost? That’s the usual metric machines are listed by.

I looked in to it 4 months ago the cheepest service I could find was 2500 usd.

That seems expensive. I got a personal sequence done (at 15x) four years ago for 750 usd. It was part of a group deal so maybe it isn't relevant to your search.

Re: Nanopore MinION – $1k solid-state DNA sequencers

#65

Post by eggie »

jlebrech wrote: post #44

sequencing is only half the story, after this we'll have software to find out allergies or perfect diets, etc..

Software is only 1% of the story. We need reliable public data from many people linking genomes, diet, life history, and phenotype to do the other 49%.

Re: Nanopore MinION – $1k solid-state DNA sequencers

#66

Post by jacquesm »

eggie wrote: post #65
jlebrech wrote: post #44

sequencing is only half the story, after this we'll have software to find out allergies or perfect diets, etc..

Software is only 1% of the story. We need reliable public data from many people linking genomes, diet, life history, and phenotype to do the other 49%.

Then you're still only at 50%...

Re: Nanopore MinION – $1k solid-state DNA sequencers

#67

Post by callesgg »

eggie wrote: post #64
callesgg wrote: post #27

Earlier quoted context omitted.

I looked in to it 4 months ago the cheepest service I could find was 2500 usd.

That seems expensive. I got a personal sequence done (at 15x) four years ago for 750 usd. It was part of a group deal so maybe it isn't relevant to your search.

Was it a full sequence?

Did you get it back as a file?

Re: Nanopore MinION – $1k solid-state DNA sequencers

#68

Post by sp332 »

zmmmmm wrote: post #59
eggie wrote: post #51

Earlier quoted context omitted.

> 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 si…

I think you are not sufficiently recognising how much structural variation can be resolved from short reads. There is certainly some that can't but a large proportion can be with the right tools.

"No human genome has ever been completely sequenced" https://news.ycombinator.com/item?id=15534325 There are a lot of gaps where the amount of repetition makes it impossible to reassemble a complete picture from tiny fragments.

Re: Nanopore MinION – $1k solid-state DNA sequencers

#69

Post by comstock »

eggie wrote: post #62
comstock wrote: post #53

Earlier quoted context omitted.

I’d agree with you, that long reads would be useful if the error rate wasn’t so shockingly bad. There is, likely value in long reads, but what non-niche research applications are there for highly error’d reads that justify a valuation of several billion dollars?

The per base error rate is bad. In the case of pacbio, this error process approximates white noise, and so you can deal with it perfectly by increasing read coverage. Things are somewhat complicated with the nanopore tech described in this post, as errors may be correlated due to the way the basecalling is done, but in practice it's nearly as big a problem as you think it is. For things approaching a read length the…

That might be the case if the throughput wasn’t so low and the error rate wasn’t so high.
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