454 vs Solexa

ramunas · 01-22-2008, 03:47 PM

Recently I came across a biotech-sequencing company in Germany - GATC - which offers services on 3 new-generation seq platforms - Solexa (Illumina), 454 (Roche) and Solid (ABI) (also conventional Sanger).
http://www.gatc-biotech.com/en/seque...g.php?navid=22

That "3 in 1" service was quite strange finding for me

- what is the point of having all these platforms?
Could anyone briefly explain the main differences between these platforms, mainly 454 and Solexa, mostly in the range of applications, specificity and cost. Are these 3rd generation sequencing platforms already applied in diagnostics?

Would be very grateful indeed,

Best wishes,
--
Ramunas J.

www.cancer-genetics.com

bioinfosm · 02-01-2008, 01:22 PM

THats for a center like GATC to answer .. why they use all 4?
Or how do they recommend a particular technology over the other, considering they use different ones depending on the project goal.

There is a lot of comparison/benchmarking to be done ... to clearly spill out the error rates of these platforms, the real usable sequence they produce; and even the downstream methods of alignment, assembly, and variation prediction!

this sounds very reasonable to the current scenario - 'you have the genome sequenced, now use IT'

govind · 02-02-2008, 07:16 AM

I came across these articles. Explains in detail the 3 sequencing technologies (SOLiD, 454 and Genome Analyzer System ).

http://www.in-sequence.com/issues/2_.../144249-1.html

and

[Admin: link removed]

-Govind Rao

ECO · 02-02-2008, 10:03 AM

Hi govind,

Thanks for the links. I've removed the second link to in-sequence for reasons that I will send to you in a PM.

-=Eric

sci_guy · 04-14-2008, 11:10 PM

Roche will release upgraded comsumables under the moniker FLX HD in H2 2008. 0.5 Gb/run.
Illumina are releasing the GA-2. 1.5Gb/run. These innovations change the Illumina/Solexa vs. Roche/454 debate a little. Contact your reps about these product upgrades.

cabauser · 08-12-2008, 04:44 AM

GATC is a service provider. So it makes sense to have as many technologies as possible available to meet the needs of scientists who all have different types of projects. In a word -Flexibility

bbjdy · 12-16-2008, 07:21 AM

Hi Ramunas,
For de novo assembly (without a reference sequence), 454 is used because of the long reads (up to 400 bp now with a titanium run) which make de novo assembly possible. While for re-sequencing (when a reference sequence OR previously generated 454 data is available) you'd rather use GA (short reads but much more data in total, and cheaper than 454)
GATC is an experienced service provider for sequencing, they also combine different nextgen technologies according to your project needs.
For our project, we want to sequence BACs containing both direct and inverted repeats. They will combine both 454 and GA sequencing technologies (possibly with different sizes of paired-end libraries), and the combination should give us much more reliable data than if only one of both would be used. They have assembly software to combine data from 454, solexa and sanger sequencing. The GA data (short reads, but much more data) can be 'mapped' on the '454 contigs'...
So I am convinced that combining different nextgen platforms can be very interesting for some projects.

wjeck · 03-17-2009, 03:49 PM

This looks like an old thread but I can't help but add a little shameless self promotion. A group of my colleagues worked hard to put together a system for 454 and GA assembly to perform de novo sequencing of bacterial genomes.

http://genome.cshlp.org/content/19/2/294.long

The long and the short of the story is: Illumina has fairly low error rates but short reads, while 454 brings long reads to the table, but with considerable homopolymer problems. They also seem to have non-overlapping sequencing biases, so that using two technologies covers more of the genome than the same quantity of sequencing with a single technology. Proper synthesis of the two data sets provides a more accurate genome with much larger contigs.

Susanne · 11-05-2009, 07:46 AM

I also think to have ssen more on comparisons somewhere on seqanswers, but also GATC offers info on their page:
http://www.gatc-biotech.com/en/sequencing.html
At least it mentions in part for what they use which technology (reseq. vs. de novo seq. vs. transcripome/metagenome seq. etc.) - thereby allowing some conclusions...

Victory · 11-26-2009, 08:10 AM

Are there anyone have information about price of sequencing per Mb for each platform? I got one from UCR website but it have only price for single end read. I also need information about pair end read especially illumina platform.

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01-22-2008, 03:47 PM	#1
ramunas Junior Member Location: Lithuania Join Date: Nov 2007 Posts: 1	454 vs Solexa Recently I came across a biotech-sequencing company in Germany - GATC - which offers services on 3 new-generation seq platforms - Solexa (Illumina), 454 (Roche) and Solid (ABI) (also conventional Sanger). http://www.gatc-biotech.com/en/seque...g.php?navid=22 That "3 in 1" service was quite strange finding for me - what is the point of having all these platforms? Could anyone briefly explain the main differences between these platforms, mainly 454 and Solexa, mostly in the range of applications, specificity and cost. Are these 3rd generation sequencing platforms already applied in diagnostics? Would be very grateful indeed, Best wishes, -- Ramunas J. www.cancer-genetics.com

02-02-2008, 07:16 AM	#3
govind Junior Member Location: India Join Date: Feb 2008 Posts: 1	I came across these articles. Explains in detail the 3 sequencing technologies (SOLiD, 454 and Genome Analyzer System ). http://www.in-sequence.com/issues/2_.../144249-1.html and [Admin: link removed] -Govind Rao Last edited by ECO; 02-02-2008 at 10:02 AM. Reason: Removed link...

11-05-2009, 07:46 AM	#9
Susanne Member Location: Germany Join Date: Aug 2009 Posts: 33	GATC webpage I also think to have ssen more on comparisons somewhere on seqanswers, but also GATC offers info on their page: http://www.gatc-biotech.com/en/sequencing.html At least it mentions in part for what they use which technology (reseq. vs. de novo seq. vs. transcripome/metagenome seq. etc.) - thereby allowing some conclusions...

02-01-2008, 01:22 PM	#2
bioinfosm Senior Member Location: USA Join Date: Jan 2008 Posts: 482	THats for a center like GATC to answer .. why they use all 4? Or how do they recommend a particular technology over the other, considering they use different ones depending on the project goal. There is a lot of comparison/benchmarking to be done ... to clearly spill out the error rates of these platforms, the real usable sequence they produce; and even the downstream methods of alignment, assembly, and variation prediction! this sounds very reasonable to the current scenario - 'you have the genome sequenced, now use IT'

02-02-2008, 10:03 AM	#4
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Hi govind, Thanks for the links. I've removed the second link to in-sequence for reasons that I will send to you in a PM. -=Eric

04-14-2008, 11:10 PM	#5
sci_guy Member Location: Sydney, Australia Join Date: Jan 2008 Posts: 83	Roche will release upgraded comsumables under the moniker FLX HD in H2 2008. 0.5 Gb/run. Illumina are releasing the GA-2. 1.5Gb/run. These innovations change the Illumina/Solexa vs. Roche/454 debate a little. Contact your reps about these product upgrades.

08-12-2008, 04:44 AM	#6
cabauser Junior Member Location: Germany Join Date: Aug 2008 Posts: 3	GATC is a service provider. So it makes sense to have as many technologies as possible available to meet the needs of scientists who all have different types of projects. In a word -Flexibility

12-16-2008, 07:21 AM	#7
bbjdy Junior Member Location: Belgium Join Date: Oct 2008 Posts: 3	Hi Ramunas, For de novo assembly (without a reference sequence), 454 is used because of the long reads (up to 400 bp now with a titanium run) which make de novo assembly possible. While for re-sequencing (when a reference sequence OR previously generated 454 data is available) you'd rather use GA (short reads but much more data in total, and cheaper than 454) GATC is an experienced service provider for sequencing, they also combine different nextgen technologies according to your project needs. For our project, we want to sequence BACs containing both direct and inverted repeats. They will combine both 454 and GA sequencing technologies (possibly with different sizes of paired-end libraries), and the combination should give us much more reliable data than if only one of both would be used. They have assembly software to combine data from 454, solexa and sanger sequencing. The GA data (short reads, but much more data) can be 'mapped' on the '454 contigs'... So I am convinced that combining different nextgen platforms can be very interesting for some projects.

03-17-2009, 03:49 PM	#8
wjeck Member Location: Chapel Hill, NC Join Date: Mar 2009 Posts: 39	This looks like an old thread but I can't help but add a little shameless self promotion. A group of my colleagues worked hard to put together a system for 454 and GA assembly to perform de novo sequencing of bacterial genomes. http://genome.cshlp.org/content/19/2/294.long The long and the short of the story is: Illumina has fairly low error rates but short reads, while 454 brings long reads to the table, but with considerable homopolymer problems. They also seem to have non-overlapping sequencing biases, so that using two technologies covers more of the genome than the same quantity of sequencing with a single technology. Proper synthesis of the two data sets provides a more accurate genome with much larger contigs.

11-26-2009, 08:10 AM	#10
Victory Member Location: Pennsylvania Join Date: Nov 2009 Posts: 13	Are there anyone have information about price of sequencing per Mb for each platform? I got one from UCR website but it have only price for single end read. I also need information about pair end read especially illumina platform.