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-   -   helicos vs solexa (http://seqanswers.com/forums/showthread.php?t=20466)

joskee 05-31-2012 06:20 AM

helicos vs solexa
 
Hallo all,

What I allways wanted to know is why you need to add the nucleotides one by one when using helicos. I know they use the same dye for each nucleotide, but why is this? Why not use 4 different dyes like when using solexa you can add all 4 labeled nucleotides at the same time.

Is this because in helicos you did not have an amplification step and less DNA (no clustering) and thus you need to be more "carefull" with measuring the fluorescence?


Thanks in advance

Kletz_AUS 05-31-2012 06:48 AM

Hello joskee. Are you currently using a Heliscope?

krobison 05-31-2012 12:08 PM

Probably an imaging issue; you can always achieve higher resolution imaging only a single color than 4. If they needed that edge in resolution, that could have been the reason.

joskee 05-31-2012 02:20 PM

Quote:

Originally Posted by Kletz_AUS (Post 74835)
Hello joskee. Are you currently using a Heliscope?

No I am not.
I am currently figuring out what the best technique would be to buy in the near future.

pmiguel 06-02-2012 10:43 AM

Quote:

Originally Posted by joskee (Post 74909)
No I am not.
I am currently figuring out what the best technique would be to buy in the near future.

I did not think Heliscopes were available for sale any longer.

Illumina may have the IP locked up on sequencing with 4 color dye-terminators at high density.

--
Phillip

joskee 06-03-2012 12:33 AM

:confused:
Quote:

Originally Posted by pmiguel (Post 75074)
I did not think Heliscopes were available for sale any longer.

Illumina may have the IP locked up on sequencing with 4 color dye-terminators at high density.

--
Phillip

:confused:
Where did you get that news from?

ANd what does an IP locked up mean?

krobison 06-03-2012 07:16 AM

IP locked up means strong patent position. Lasergene and Intelligent Biosystems are both proposing systems in this space, so they at least think there is room here.

scbaker 06-03-2012 12:19 PM

Helicos stopped selling new instruments quite a while ago:

From a GenomeWeb article in May 2011:
"The company stopped production of its Helicos Systems sequencer in the first half of 2010 as it shifted its focus to becoming a molecular diagnostics shop."

You can still use them as a service provider, but even their current customers are getting frustrated with their ability to maintain instruments in the field (let alone provide new ones).

There are lots of choices when looking to buy a sequencing platform, but Helicos really isn't one of them. (You can check out BlueSEQ for descriptions of the various other platforms/technologies for sale.)

joskee 06-04-2012 08:58 AM

Quote:

Originally Posted by krobison (Post 75105)
IP locked up means strong patent position. Lasergene and Intelligent Biosystems are both proposing systems in this space, so they at least think there is room here.

Ah ok.

Quote:

Originally Posted by scbaker (Post 75112)
Helicos stopped selling new instruments quite a while ago:

From a GenomeWeb article in May 2011:
"The company stopped production of its Helicos Systems sequencer in the first half of 2010 as it shifted its focus to becoming a molecular diagnostics shop."

You can still use them as a service provider, but even their current customers are getting frustrated with their ability to maintain instruments in the field (let alone provide new ones).

There are lots of choices when looking to buy a sequencing platform, but Helicos really isn't one of them. (You can check out BlueSEQ for descriptions of the various other platforms/technologies for sale.)

Aha, I see.
To be honest, I dont know a lot about these things. I am "in charge of the money" and the departement is looking into buying a sequencer together with another department and thats why I am looking into all these techniques.

But thanks for the information, helicos is allready out then.

pmiguel 06-04-2012 09:18 AM

Quote:

Originally Posted by joskee (Post 75183)
Ah ok.



Aha, I see.
To be honest, I dont know a lot about these things. I am "in charge of the money" and the departement is looking into buying a sequencer together with another department and thats why I am looking into all these techniques.

But thanks for the information, helicos is allready out then.

I seem to remember that Illumina (Solexa, actually) had a patent on reversible terminators. Not simultaneous 4 color chemistry. I had that wrong.

Helicos is essentially dead as an instrument supplier.

Currently the lead instrument in this arena is the Illumina HiSeq2000 (actually HiSeq2500 by the time you would purchase an instrument.) This type of instrument used to be called a "Solexa" -- but that terminology is rarely used any more. The company, Solexa, was purchased by Illumina years ago.

Illumina has essentially crushed all competitors at this point, although there are a few possible contenders that might arrive by year's end. The strongest would be the Life Technologies Proton Torrent. Life also has an upgrade to a current instrument (SOLiD 5500XL) called "wildfire" that could conceivably put it back in contention. But I doubt it.

Finally, Oxford Nanopore Technologies (ONT) threatened to release a 4th generation instrument, the "GridIon" this year. It is both the most vaporous and the most interesting of potential sequencers. Were it actually capable of delivering on what ONT was suggesting it would, I think all other players would be relegated to niche markets, if not driven out of business altogether.

--
Phillip

Elcannibal 06-07-2012 10:02 AM

This thread is nightmarish to me... It's hard to fantom how decisions are being made in research. Frankly, if you take the 'money' decision, it would be a basic, very basic decision to settle on 2-3 systems based on your needs. A system that no one has bought, that will go bankrupt or based on promises is like burning money. 500,000$ of malaria nets might bring more solutions to the world than another sequencer PO... Sorry for my rant. I'm guessing that is is public money to boot...

joskee 06-07-2012 11:02 PM

Quote:

Originally Posted by Elcannibal (Post 75578)
This thread is nightmarish to me... It's hard to fantom how decisions are being made in research. Frankly, if you take the 'money' decision, it would be a basic, very basic decision to settle on 2-3 systems based on your needs. A system that no one has bought, that will go bankrupt or based on promises is like burning money. 500,000$ of malaria nets might bring more solutions to the world than another sequencer PO... Sorry for my rant. I'm guessing that is is public money to boot...

You bought one from helicos?

This is indeed no good then.
Its also good for me to learn a bit more about the companies etc.. because indeed, imagine you buy something (pretty expensive) and 1 year later the company is gone for example..

Elcannibal 06-08-2012 03:44 PM

My 5 year old kid knows Helicos went under or is going, he can also give you a few predictions about where the market is going and its not up, stick to the big boys, there is only two. If you are working on human, I would even go further to tell you to just outsource your research, DNA sequencing is going the same way someone builds an IPhone, straight to cheap labor...

joskee 06-09-2012 09:39 AM

Quote:

Originally Posted by Elcannibal (Post 75765)
My 5 year old kid knows Helicos went under or is going, he can also give you a few predictions about where the market is going and its not up, stick to the big boys, there is only two. If you are working on human, I would even go further to tell you to just outsource your research, DNA sequencing is going the same way someone builds an IPhone, straight to cheap labor...

Maybe I should clarify what I ment with I take the "money decision".
It has nothing to do with poor research, on the contrary!

I am not the one who decides what machine/technology will be bought. I am just one of them that says ok or not ok, looking at the budget and based on what the scientists tell me.
(of course, I am not just alone, there are others too that will look into it)
But I always take it very serious and will invest my time in order to learn more about the technologies/companies (and this without too much influence of the researchers, just to stay objective and neutral. Its on purpose that I check the things without contacting the scientists of the lab, to stay objective).
After I did my research, there will me meetings where I listen to the scientists and hear why they want a specific type of technology.
And because I learned some of it, I am able to +- understand what they mean or why something is bad/good.
Its not a decision about 50dollar
And since this is not my area of expertise, I have to start somewhere...



BTW: bad research is where companies let the scientists decide completely or where people like me, controlling the budget dont care about the techniques and make a decision without any knowledge about the science.
There is a huge difference between a scientist buying some stuff because he/she "thinks" he/she needs it/can use it and how we check it from both sides: economically and scientifically.
You should be glad that I am willing to invest my time in the techniques rather than just being one that says ok or not ok, purely based on money without any scientifically knowledge at all (which is done in some companies, as your allready mentioned)
And I absolutely do not agree with what you said here:
Quote:

Frankly, if you take the 'money' decision, it would be a basic, very basic decision to settle on 2-3 systems based on your needs
Also: its no public money... its money from the lab and needs to be spent very very well.

But that being said, I misinterpreted your first comment, probably leading to your second comment and my comment now.

pmiguel 06-09-2012 12:43 PM

In that case, the main point I would emphasize is that the next gen sequencing market is insanely volatile at the moment and looks to remain that way for the foreseeable future. Any instrument you buy now will likely be obsolete within 3 years. The main players try to buffer this reality a bit by offering "upgrades" of one type or another at intervals. These might be free, or cost $50-$100K.

But, I have to say, it is possible that 1 year from now 4th generation sequencers may obsolete all the 2nd generation sequencers that are in use now. Or the 4th generation sequencers may fizzle like the 3rd gen sequencers (helicos and to a lesser extent PacBio).

However, "playing it safe" by avoiding the technology altogether is a mistake as well. I have pointed out before that many of the 2nd gen sequencers can produce more sequence/unit of time than the entire world capacity 5 years ago. Think of what that means for the sorts of projects now possible.

I think Elcannibal is reacting to your invoking a nearly dead company that probably shipped no more than a dozen instruments in the same sentence with Illumina, who has held market dominance for several years now. Really, the message here is that if your scientists are recommending buying "either a Solexa or a Heliscope" then they have no idea what they are talking about. It would be an indication that you would be starting from the ground up -- from zero expertise, were you to purchase a sequencer of this sort.

If this is the case, I would highly recommend looking at one of the two smaller "bench top" next generation sequencers. The Illumina MiSeq or the Life Technologies Ion Torrent. These instruments give you enormous sequencing power at maybe 1/5th the initial cost of the larger Illumina HiSeq. Or, as ElCannibal suggests, use a commercial service instead.

If it comes down to price per base though, the Illumina HiSeq is king at the moment. But look at the sequence output of that monster and ask what sorts of assays require it. Correct answers would include expression analysis of large numbers of samples using RNAseq and genome resequencing/genotyping by sequencing.

Good luck.

--
Phillip

joskee 06-10-2012 05:44 AM

Actually they have not told me that helicos is an alternative.. None of the scientist spoke about it... I am assuming this is because of what you guys tell me here..
I just stumbled upon the helicos technologies and wondered why etc...
As I said: I try to understand the techniques too.

And yes, its possible we will wait even longer.. this is also why I (and others) are taking our time in making a decision. Especially because it does look like that sending samples away, and let a third party sequence it, might be even cheaper...

Its just simple really: its because of my own interest I am learning about these technologies. Its not me, that will make the scientific decision.


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