Follow Slashdot blog updates by subscribing to our blog RSS feed

 



Forgot your password?
typodupeerror

Comment Re:nanopore tech still has accuracy problems (Score 1) 33

Yes, absolutely. However, the nanopore sequencer has to have more than one limited-applicability advantage for it to be commercially successful against competitors. Just consider seriously for a minute what has actually been described (not hyped about) in this paper.
    1) A mobile lab in a suitcase including sequencer - yes, that's awesome
    2) Deployed to a region experiencing an outbreak
        - ok, can be useful, but how many outbreaks occur every year that actually benefit from on-site sequencing
        - in the case of Ebola, which spreads and mutates quickly, the advantage may be very real, but Zika? the flu? not so sure
        - is the advantage enough to offset the tremendous cost compared to alternatives?
    3) They did sequence a segment of the viral genome (not the whole genome) and successfully call base mismatches
        - but they didn't call indels
        - they ignored homopolymer regions and the ends of their amplicons
        - they did get some useful information, but there were samples that they couldn't successfully analyze after sequencing

So in the end, it is a sequencer that can be deployed to remote villages, provided you have a very limited set of analyses you intend to do, and you don't care about the cost. But is that enough to be commercially viable and displace competitors? I don't think so.

I'm not trying to rag on Oxford Nanopore, don't get me wrong. If they really could reliably sequence whole genomes fast and with minimal preparation from a usb stick, I would definitely jump on the bandwagon. I'm just tired of all the hype. They've been promising these breakthroughs for more than a decade now, but they have yet to deliver. Meanwhile other companies, namely PacBio, have appeared and been very successful at providing long reads at an affordable cost, so I'm not holding my breath for ONP.

Comment Re:nanopore tech still has accuracy problems (Score 1) 33

though if necessary you could presumably do many additional passes to bring the error rate down further.

In its present state, not really. The biggest problem with nanopore data right now is systematic errors in homopolymer regions. These can't be easily corrected out with higher coverage. Incidentally, some of the most significant mutation events are in homopolymer regions, so this is bad.

but it's more than sufficient to recognize a virus.

Correct. But you need to know more. In particular, which strain of virus? Strain variations can easily be much less than 4%.

but so long as you're taking many samples from a community you can probably make a pretty high-confidence conclusion about even SNPs

If the errors were mostly random, you are correct. That is the problem here, the errors are systematic, not random, which is why they can't be corrected out with higher coverage. The good news, though, is that if you are looking at other types of mutations, like inversions or repeat expansions, that are easier to identify than SNPs, the error rate is probably good enough.

Not perfect, but a huge improvement over simply guessing at the path of infection.

You don't have to guess. You just have to use a different sequencing technology. Almost every vendor is trying to provide a rapid sequencing service for this exact reason. Illumina has MiSeq (12-24 hrs. run time), and PacBio is always fast (run time ~3 hrs) as is Ion Torrent (run time ~2 hrs). The biggest advantage that ONP has is portability, but if you need a lab (and an Internet connection) anyway to process samples, I'm not sure that this will really play out to their favor in the long run. ONP gets a lot of awe and excitement, which leads to a lot of hype, but not a lot of practical advantages.

Comment Re:nanopore tech still has accuracy problems (Score 1) 33

Or maybe they're already doing that and accuracy plateaus at 96%

Yes, this is correct.

They're not trying to do genome-research class sequencing, they just need to identify the DNA strands of interest

Well, it does depend on what kind of downstream analysis they plan to do, but 96% is not great. That is 1 error per 25 bases. Good enough for alignment procedures to work, but definitely bad if you are looking for SNPs.

As one commenter on ONP has been stating for a while: what's the point of a portable sequencer if you have to haul around a full-size Illumina sequencer along with it to get the accuracy you need?

The nanopore's advantage in this example is the virus genome, which is a relatively small size, and a well-defined reference sequence. In its present state, the nanopore is mostly useless for larger, previously unsequenced, genomes on a cost/bp basis.

Comment Re:nanopore tech still has accuracy problems (Score 2) 33

> Base calling accuracy: up to 96%

Um, bullshit. See, this has been the problem with Oxford Nanopore since the beginning. They distract and confuse through a lot of misleading statements and media hype, which is why I can't trust any of their claims. The typical accuracy of single-pass 1D reads on real data is about 70%, about 80% on 2D reads. The 96% accuracy they are quoting on their site is after they error-correct the reads.

Comment Re:Very cool but has competition (Score 1) 33

An illumina can do many more samples in a single run, in batch. But you might not want to take it into the field and your latency would be higher since you would accumulate samples until you had enough to justify one run.

But they are still (probably) burning one nanopore per sample, so that's $900 per run (yeah, I'm sure ONP gave them a hefty discount). So the overall cost is much higher than with Illumina, but you are right about the latency. In cases where that matters, I would go with PacBio (cheaper and faster).

Another way this thing is superior is in read-length (50kbases)

Well, let's say "up to 50 kb". The average is a different story, especially if you need to get the higher-quality 2D reads for your downstream analysis. ONP has been promising >100 kb reads for a long time but have yet to deliver. Much better than Illumina, as you say, but not better than PacBio.

Comment Re:This breaks my brain. (Score 3, Informative) 33

I'm an outsider, so I've just gotta be misunderstanding something.

Well, like pretty much all press coverage of the Oxford Nanopore sequencer, there is a ton of hype but questionable value. I'll give the nanopore portability. It is an incredible feat compared to the large sequencers (even the benchtop MiSeq). But here's the thing:
    1) The accuracy is terrible. This is especially important when you are looking at SNP variants. You need accuracy.
    2) The sequencer may be portable, but data analysis in this version currently uses a cloud service that (obviously) requires an Internet connection, so I'm not sure the hype about service in rural areas is really that great.
    3) The throughput is ok, but not great. For virus genomes this might be fine, but for bacterial and larger genomes, it's a no go.
    4) The speed isn't all that great. It's around 24 hrs. to complete a 2D run. That is right in line with what is offered by other sequencers.
    5) Yes, you DO need a library prep, contrary to what the proponents claim. It might be a little bit simpler than some conventional protocols, but you cannot just drop DNA into the pore.

All of this, in my mind, comes down to two features that matter most for any sequencer: cost and speed.

Cost:
The best cost/bp currently, by far, comes from Illumina technologies. This will never compete with that. That said, Oxford Nanopore has an advantage in read length that Illumina will never have. However, PacBio has been competing in the read length niche for a while now and is well-established. So is the cost of Oxford Nanopore better than PacBio? Cost is mostly a function of yield x read length. For PacBio, the cost of a sequencing unit (a SMRT cell) is ~$600 (the library prep cost is ~$400, but is a one-time cost for each sample). One SMRT cell yields ~0.5 - 1 Gb per run, so $0.0000006/bp (Note: this is with the older RS II system. With the newer Sequel system the throughput is better). The Oxford Nanopore site claims up to 1 Gb per chip, at $900/chip, but the reality is a bit less. Based on a recent paper where they assembled the E. coli genome with nanopore data, the proportion of actual usable data is closer to 150 Mb. So that's about 10 times the cost of PacBio sequencing.

Speed:
The Oxford Nanopore site claims they are fast, but to get the higher quality 2D reads that you need for assembly, the run times are typically about 18-24 hrs. For a MiSeq, the run time can be as low as 12 hrs, and for PacBio it is 3 hrs. So the nanopore is not really winning with speed either.

It seems to me that portability is the biggest strength of the nanopore, but the majority of groups are still going to get their sequencing done at core facilities, so I have doubts about how that will play out in the market. What they really need to focus on is cost. But everyone is doing that at the same time, so it is a hard race to keep up with.

Comment Re:Because Docker uses a Linux container (Score 1) 131

FreeBSD Jails and Linux Containers are really different beasts. Jails are great if security is your primary consideration. Hence the name: Jails effectively isolate processes and go to great lengths to prevent them from accessing anything outside the jail. Containers use separate kernel namespaces to give groups of processes separate views of kernel global variables. Security (especially with user namespaces) is a bonus, but the primary goal is efficient os-level virtualization and isolation of resources. A more apt comparison is with the BSD VPS project rather than Jails.

At a guess the jail support didn't make it.

Correct. XNU does not have support for Jails, and it likely won't because it requires some pretty severe changes to kernel data structures to make them work.

Comment Re:RAID 0 is not for anything you don't want to lo (Score 2) 73

Ummm...ok. So when your SMART detects a failing drive in your RAID0 array and you decide you want to replace it, how do you do that exactly? Oh, that's right, wipe the entire array and restore from backup, which, depending on the size of your array can take anywhere from several hours to days, more if you decided to use your array to run the OS as well. RAID0 is just a plain terrible idea, period. It doesn't matter if you don't think you need uptime, an N disk RAID0 is N times more likely to fail catastrophically as a standalone hard disk (assuming the failure rates on all of the hard disks are equal), and without redundancy getting back up and running is a long process.

Comment Re:Remember the NASA Wind Turbines? (Score 1) 184

Current blades are trucked in one piece (per blade) which is impressive to see. Three of them were parked on I-5 outside of Patterson, California a few months ago. There are a lot of net videos and photos which convey the scale.

Even at the current size they can't get through many highway interchanges and local intersections. The larger ones won't be able to ship in one piece at all.

Comment Remember the NASA Wind Turbines? (Score 4, Interesting) 184

NASA Wind Turbines approached this scale in the '80's. Unfortunately, this was a previously-unexplored area of aerodynamics for NASA, and they had mechanical stress and noise problems (including subsonics) and were all demolished. I think there was one near Vallejo, CA being taken down when I got to Pixar in '87, and one in Boone, NC, which famously rattled windows and doors.

The art has since improved. I took a ride to the top of the turbine at Grouse Mountain, that was fun! That's the only one I have heard of where you can actually get to see it from the top.

Comment Starting out with the wrong assumptions (Score 2) 165

This is starting out with the wrong assumptions.

Design a brick system that can be produced with 3-D printers, and will hold together when fabricated within the tolerances of an SLA printer. Forget FDM, it's too low precision and SLA is already achieving an equal or lower cost of manufacture compared with FDM.

LEGO is manufactured to astonishingly high precision, but I am not convinced that this is the only way to make a brick system.

Slashdot Top Deals

The Wright Bothers weren't the first to fly. They were just the first not to crash.

Working...