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-   -   Oxford Nanopore @ ASHG (http://seqanswers.com/forums/showthread.php?t=24807)

GenoMax 11-09-2012 04:49 AM

Quote:

Originally Posted by TonyBrooks (Post 88923)
Maybe ONT have learnt from PacBio's mistakes. Remember the anticlimax when you first saw PacBio data?

There is some truth to that. Unfortunately this is starting to feel like "Duke Nukem Forever".

GW_OK 11-09-2012 07:54 AM

I think they could release something and just put a giant red asterisk next to it saying this is only really, really preliminary data, really.

Any data at all would, I think, get people to cut them some slack.

earonesty 11-09-2012 09:56 AM

Quote:

Originally Posted by TonyBrooks (Post 88923)
Maybe ONT have learnt from PacBio's mistakes. Remember the anticlimax when you first saw PacBio data?

Nanopore error rate is around 4% ~Q14, or at least it was 9 months ago.
The problem is we've all been spoilt by Illumina SBS and will see anything with < Q30 (or even Q20). They've gone on record saying they won't release anything until error is <1% (which is probably nearer the acceptable level). How far away from that they are is anyone's guess at the moment.

PacBio reads, at Q8, are still quite useful for scaffolding assemblies. Crazy to hold back data when there are lots of people who could make use of long Q14 reads right now.

BadDNA 11-09-2012 11:49 AM

Let us scaffold!
 
Quote:

Originally Posted by earonesty (Post 88978)
PacBio reads, at Q8, are still quite useful for scaffolding assemblies. Crazy to hold back data when there are lots of people who could make use of long Q14 reads right now.

I agree completely!

DaleYuzuki 11-10-2012 06:18 AM

If anyone's interested, I wrote up this post after talking with Oxford and several others at ASHG.

Really too bad that there wasn't any firm specifications or pricing.

Dale

TonyBrooks 11-12-2012 06:49 AM

Quote:

Originally Posted by earonesty (Post 88978)
PacBio reads, at Q8, are still quite useful for scaffolding assemblies. Crazy to hold back data when there are lots of people who could make use of long Q14 reads right now.

The problem is that scaffold runs for de novo are so niche in the grand scheme of things. The real money will be in resequencing, RNA-Seq, ChIP-Seq etc. As a core group, I'd say 99% of things we get asked to do fall into those categories. There's still a long way to go for ONT until it becomes a viable alternative.
Q14 is only really of value when you have a bunch of short read Q30s you can pin to the scaffold.

ECO 11-12-2012 11:22 PM

Quote:

Originally Posted by DaleYuzuki (Post 89027)
If anyone's interested, I wrote up this post after talking with Oxford and several others at ASHG.

Really too bad that there wasn't any firm specifications or pricing.

Dale

That ONT post mentioned Ion Torrent's party more than it did ONT. Heh.

GW_OK 11-13-2012 06:59 AM

Dale's post does have an insightful comment at the bottom. How much of the silence from ONT is because they don't have anything to show and how much is due to their current arbitration with Illumina? Maybe they're just playing it close to the vest?

seqnextgen 11-13-2012 10:04 PM

Quote:

Originally Posted by TonyBrooks (Post 89086)
The problem is that scaffold runs for de novo are so niche in the grand scheme of things. The real money will be in resequencing, RNA-Seq, ChIP-Seq etc. As a core group, I'd say 99% of things we get asked to do fall into those categories. There's still a long way to go for ONT until it becomes a viable alternative.
Q14 is only really of value when you have a bunch of short read Q30s you can pin to the scaffold.

Maybe, but once de novo assembly is really available with a reasonable price, I believe it is the way to go. Ever wonder where those "copy number variants" are in a genome. It might be hard to believe that where they are is not important.

pmiguel 11-14-2012 04:43 AM

The other major claim is that no library construction (or even DNA purification) is required. That would immediately put these devices in their own league. That makes HiSeqs and Torrents niche instruments.

Of course there is the weaselly "sample needs 10 base single stranded leader" statement. Not sure what that means. Like you need a cos site digested with lambda terminase? Or you can just heat your sample a little to melt the terminii?

--
Phillip

seqnextgen 11-14-2012 06:36 AM

Quote:

Originally Posted by pmiguel (Post 89217)
The other major claim is that no library construction (or even DNA purification) is required. That would immediately put these devices in their own league. That makes HiSeqs and Torrents niche instruments.

....

--
Phillip

I think ECO can probably comment on this better. All I know is once you go to single molecule world, any impurity can kill the sequencing mechanism / basecalling accuracy easily. Any "single molecule" impurities including any ion that one does not anticipate during engineering phase is the enemy, so, good luck for the "no sample preparation" claim. (Not saying it can not be simple, but sequencing DNA in blood with zero sample-prep to get high throughput results? one can judge that with common sense...)

Amiga 11-15-2012 06:32 PM

The grand scheme of things of for-profit sector is targeted resequencing for diagnostic. The only thing ONT are proposing that could be useful to them is the no sample prep at all. And I am having a hard time believing that.

While a $100 disposable cartridge would be nice too, especially to forensic and DTC providers, a Q14 isn't useful for any of them.

I agree with other people prediction that ONT will be the next PacBio. It's noble to claim that they will delay their launch until they get Q30, but they need investors, and the current ones will eventually want to cash in. PacBio was able to hype and overhype for 5 years. How much longer is it going to be for ONT?

seqnextgen 11-15-2012 11:10 PM

Just a quick reminder of some facts. For ONT to be next PacBio, at least they need to show some data and publish papers in NEJM from sample to print within weeks, not once, but twice. And, they will also need to publish DNA sequencing data/DNA modification data in Nature / Nature Biotech to show important biological results that can not be resolved by 2nd gen. sequencing / Sanger sequencing, etc. (Not just nucleotide identification. DNA sequencing is not about identifying bases/short segments. DNA sequencing should be about efficiently linking long range information...) Commercially successfully or not, the publications and real data already help to reveal some new biology. Until nanopore is no longer nanovapor, there is no fair comparison.

BBoy 02-15-2013 01:30 AM

Quote:

Originally Posted by seqnextgen (Post 89400)
Just a quick reminder of some facts. For ONT to be next PacBio, at least they need to show some data and publish papers in NEJM from sample to print within weeks, not once, but twice. And, they will also need to publish DNA sequencing data/DNA modification data in Nature / Nature Biotech to show important biological results that can not be resolved by 2nd gen. sequencing / Sanger sequencing, etc. (Not just nucleotide identification. DNA sequencing is not about identifying bases/short segments. DNA sequencing should be about efficiently linking long range information...) Commercially successfully or not, the publications and real data already help to reveal some new biology. Until nanopore is no longer nanovapor, there is no fair comparison.

Well said...

paulk 02-15-2013 06:47 PM

Quote:

Originally Posted by TonyBrooks (Post 89086)
The problem is that scaffold runs for de novo are so niche in the grand scheme of things.

Not really; I'd love to be able to quickly map out cancer genome rearrangements and a 4% error rate wouldn't bother me for that purpose.

I wonder what updates will come out next week at AGBT...

seqnextgen 03-03-2013 11:00 AM

Quote:

Originally Posted by paulk (Post 96576)
Not really; I'd love to be able to quickly map out cancer genome rearrangements and a 4% error rate wouldn't bother me for that purpose.

I wonder what updates will come out next week at AGBT...

AFAIK, nothing..... no data, no status update, not even a cool USB sequencer full with data found in a bar

krobison 03-04-2013 05:49 AM

Quote:

Originally Posted by seqnextgen (Post 98034)
AFAIK, nothing..... no data, no status update, not even a cool USB sequencer full with data found in a bar

What? You weren't out on the strand digging through sand like a madman? :)

BBoy 03-04-2013 10:39 PM

Quote:

Originally Posted by krobison (Post 98066)

Apparently we have all been asleep at the wheel. The minion has been out for decades, the first model has even made it to a museum:
http://core-genomics.blogspot.com/20...announced.html

GW_OK 03-06-2013 07:47 AM

Quote:

Originally Posted by krobison (Post 98066)

I confess that I did stroll through the beach area around the suites (on my way to my next meeting! I was going through there anyway, honest!) looking for disturbed sand patches.

I should have been stalking the bar, apparently.

seqnextgen 03-06-2013 07:47 AM

Quote:

Originally Posted by krobison (Post 98066)

I thought it was a joke originally, obviously, pathogenomics did find a MiniIon in AGBT. This is probably more comprehensive non-update one can find now
http://pathogenomics.bham.ac.uk/blog...-at-agbt-2013/


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