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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

#101

Post by rotexo »

daemonk wrote: post #90
rotexo wrote: post #76

One thing I'm excited for here is targeted sequencing using read-until. In this method, you monitor the current trace coming off of individual pores, and if you determine that the DNA in that pore is not part of your sequence of interest, you can reverse the voltage to remove the DNA and start sequencing another molecule. I think this will open up a lot of applications for human genomics. If you're interested in Oxfo…

There is a group in UK (Matt Loose's group) that I think is working a lot on read-until. I haven't really kept up with it. I think the key for read-until to work is ultimately probably going to be better hardware as you need to be able to analyze the trace signal and compare it against a database fast enough to tell the device to kick it out. There are plenty of software optimizations that can be done to compress the…

Also as a biologist by trade and an audio dsp nut by hobby I loved that they were using algorithms initially developed for music information retrieval to extend the capabilities of a sequencing instrument.

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

#102

Post by dnautics »

folli wrote: post #22
atg_gcg_aca_aca wrote: post #16

Earlier quoted context omitted.

A few years ago, the sequencing field was really excited for this platform as an alternative/competitor to Illumina. Unfortunately, the MinION platform has never been able to generate enough high-quality data for most eukaryotic sequencing use cases. The MinION still has it's niche... long read sequencing can resolve problematic regions of the genome, and the minION is the only option for rapid sequencing in the fiel…

Where do you see PacBio?

pacbio has this fundamental problem that it's a single molecule process (as does MinION) and deconvoluting errors becomes a problem of unit parallelization.

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

#103

Post by searine »

comstock wrote: post #100
searine wrote: post #71

Earlier quoted context omitted.

>The error rate is stupidly high (somewhere between 10 and 20%) The Insertion/deletion error rate is 20-30%. The point mutation error rate is something 0.1-1% (higher than HiSeq but not crazy high). This means with a semi-decent reference genome you should be able to do re-sequencing fairly accurately. It also means, that in conjunction with HiSeq reads you can do cheap genome assembly, using the HiSeq reads for cove…

Do you have a citation for this? Because this is not my understanding.

No citation, just personal experience aligning the data and comparing it directly to a hiSeq run of the same DNA.

I was able to get about 1-10% mutation rate, with a median of about 1.5%. Rate depending on quality of the run. In general it was on par with PacBio.

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

#104

Post by daemonk »

comstock wrote: post #100
searine wrote: post #71

Earlier quoted context omitted.

>The error rate is stupidly high (somewhere between 10 and 20%) The Insertion/deletion error rate is 20-30%. The point mutation error rate is something 0.1-1% (higher than HiSeq but not crazy high). This means with a semi-decent reference genome you should be able to do re-sequencing fairly accurately. It also means, that in conjunction with HiSeq reads you can do cheap genome assembly, using the HiSeq reads for cove…

Do you have a citation for this? Because this is not my understanding.

I can add to this with my anecdotal evidence. In my experience (looked at ~15gb of basecalled data total), there is a large amount of indel errors.

The mismatch rate is much lower. But it's hard to calculate exactly the mismatch rate when the indel rate is so high.

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

#105

Post by cgravill »

aghillo wrote: post #31

Can we ever imagine dna sequencing been done like a remoter sensor? E.g. automated sampling for e(environmental) dna,in-situ sequencing (single and multi species targeting), results transmitted back wirelessly. A biodiversity IoT system?

There's a Microsoft Research project that does something like this with mosquitoes for disease management: https://www.microsoft.com/en-us/research/project/project-pre...

(note: I work at MSR, but on other projects)

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

#106

Post by maxander »

comstock wrote: post #99
bayesian_horse wrote: post #85

Earlier quoted context omitted.

Virtually all applications can benefit from long reads. There are already hybrid assemblers out there which take Illumina, Pacbio and Nanopore reads. The long reads tie the short reads together, whereas the short reads improve the accuracy. The area where DNA sequencing will first be revolutionizing clinical practice is in sequencing pathogens for sake of identification. In these instances nanopore sequencing rules,…

Most clinical applications don’t need long reads. Pathogen identification from short reads is easy. Blood tests for cancer, and NIPT (which will likely be the first big applications) both use fragmented DNA in the blood, so long reads are not useful. Depth (lots of sequencing) and quality are far more important.

It's worth noting that those clinical applications were developed when technology didn't allow long reads, so "clinical applications don't need long reads" is at present a truism. There may be potential applications that require long reads that simply couldn't have been invented yet (albeit I haven't the slightest what those would be.)

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

#107

Post by comstock »

maxander wrote: post #106
comstock wrote: post #99

Earlier quoted context omitted.

Most clinical applications don’t need long reads. Pathogen identification from short reads is easy. Blood tests for cancer, and NIPT (which will likely be the first big applications) both use fragmented DNA in the blood, so long reads are not useful. Depth (lots of sequencing) and quality are far more important.

It's worth noting that those clinical applications were developed when technology didn't allow long reads, so "clinical applications don't need long reads" is at present a truism. There may be potential applications that require long reads that simply couldn't have been invented yet (albeit I haven't the slightest what those would be.)

Yes, but I would say quality is most important in almost all cases. Well, quality being defined as The most compelling near term applications (NITP etc) use fragmented DNA, and long reads will have no benefit here.

So, yes. Long reads are useful, but you need to have at least reasonable performance in other respects. The same thing has been seen with PacBio, who have not played well in the market, despite having a read length advantage.

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

#108

Post by michaelbarton »

GolDDranks wrote: post #21

How far away we are from a 100$ genome? I've heard that the cost/performance development rate is 'super-Moorean'.

I think we're already there. You can probably get around a $50 dollar bacterial genome by using robots and doing 384-well plates of samples at a time to get economies of scale.

A lot of the costs are outside of the sequencing itself. You have to extract the DNA from the sample and prepare that DNA for the sequencing platform you're using. These costs are both the reagents needed to do this, and also the associated labour costs, even when done at scale.

Perhaps you meant $100 human genome though? However I think roughly the same principles apply.

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

#109

Post by bayesian_horse »

comstock wrote: post #99
bayesian_horse wrote: post #85

Earlier quoted context omitted.

Virtually all applications can benefit from long reads. There are already hybrid assemblers out there which take Illumina, Pacbio and Nanopore reads. The long reads tie the short reads together, whereas the short reads improve the accuracy. The area where DNA sequencing will first be revolutionizing clinical practice is in sequencing pathogens for sake of identification. In these instances nanopore sequencing rules,…

Most clinical applications don’t need long reads. Pathogen identification from short reads is easy. Blood tests for cancer, and NIPT (which will likely be the first big applications) both use fragmented DNA in the blood, so long reads are not useful. Depth (lots of sequencing) and quality are far more important.

How long does it take to get the answer? Even if a big, expensive short read sequencing machine is in the building, it still takes a day or two to reach the necessary data.

With sepsis, every hour counts.

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

#110

Post by virusduck »

rotexo wrote: post #76

One thing I'm excited for here is targeted sequencing using read-until. In this method, you monitor the current trace coming off of individual pores, and if you determine that the DNA in that pore is not part of your sequence of interest, you can reverse the voltage to remove the DNA and start sequencing another molecule. I think this will open up a lot of applications for human genomics. If you're interested in Oxfo…

Read-until has had diminishing utility. Over the last year or so, the speed at which a read can pass through the pore has increased so that by the time you call the bases and determine what it is, the read is likely to have already passed through the pore.
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