Tech Summary: Roche's 454 GS20 / FLX / Titanium

ECO · 09-27-2008, 05:28 PM

There isn't anything here yet!

If you are interested in writing a tech summary, just post it below and I will rearrange the thread as appropriate.

Alternatively if anyone wants to post tech sheets, manuals, etc, I will write it. I just don't know enough of it beyond "pyrosequencing, picotiter plates, and a ton of beads".

Tom Bair · 10-01-2008, 07:02 AM

Needed this for something else may be incomplete or wrong but ..

400-600 million high-quality, filter-passed bases per run
10 hours
average length 400 bp
more than 1x10^6 reads

a cluster from roche is recommended for signal processing from www.pssclabs.com. It looks like image processing will still happen on the GS-FLX and 9G of cwf (wells) files need to go the the cluster

from what I can tell it is a 5 node system (20 cores) the only specs I can find say redhat with either openMPI or MPI2 (mpiexec), SunGrid as scheduler

runs will be 35GB (26GB images)

A test data-set with a configuration tester is promised soon

Rumor has it that bead breaking will be via centrifuge in the new protocol

genseq · 10-04-2008, 10:58 AM

It isn't Titanium, but it is about new pyrosequencing from Illumina:

Development of a 10Gb Pyrosequencer
Ronaghi, Mostafa
Illumina, Inc., San Diego, CA
R01 HG003571
$5.1 million (3 years)

Collaborators: Helmy Eltoukhy, Stevan Jovanovich (Microchip Biotechnologies, Inc.)

We propose to develop a low-cost 10-Gb Pyrosequencer for de novo DNA sequencing that would enable any lab to perform high-throughput genome analyses. The platform implements automated sample preparation scheme combined with massive Pyrosequencing, which will potentially enable mammalian genome sequencing in a single run. A sensitive CMOS image sensor has been designed and fabricated specialized for Pyrosequencing chemistry, which is integrated with fluidic platform. Each well in the fluidic platform has a pixel on CMOS for detection of light signal generated from Pyrosequencing. The integrated chip will have a 2-megapixel CMOS, each pixel located on a single well enabling 2 million sequencing on each chip. Sixteen of such chips are set up on a board to develop a 32-million wells Pyrosequencer which potentially enable sequencing of more than 10 gigabase of genomic DNA. The raw data are immediately collected and assembled with our developed algorithms. We envision that the genome sequencing of mammalian genome to be reduced below $100,000 level for large-scale genome sequencing projects.

bioinfosm · 10-15-2008, 01:32 PM

I am confused by this .. "pyrosequencing from illumina" !

monad · 11-21-2008, 08:24 AM

Quote:

Originally Posted by bioinfosm

I am confused by this .. "pyrosequencing from illumina" !

Confused here too.
Illmunia currently produces 15-20GB from single run of paired-end already.
Protocol will be available sometime early next year.

ECO · 11-21-2008, 08:32 AM

Quote:

Originally Posted by bioinfosm

I am confused by this .. "pyrosequencing from illumina" !

Quote:

Originally Posted by monad

Confused here too.
Illmunia currently produces 15-20GB from single run of paired-end already.
Protocol will be available sometime early next year.

They bought Avantome.

SeqWhiskey · 06-10-2009, 03:29 PM

Look out for the SV prep on titanium. There is a pretty serious typo under the DNA capture step. 3.2.7 the volume to evenly distribute capture beads is off. It says 40ul per rxn, it's really more like 70+ul. In fact completely ignore this section and prep each rxn in individual 1.7ml tubes. The roche tech agrees with me... just wash with 3-400ul of cap bead wash buff so you don't run out.... Then again, does Ti even work as advertised?

edge · 10-04-2009, 10:55 PM

Hi,

You have already summary out the tech of Roche's 454 GS20 / FLX / Titanium?
I interesting about it too

Quote:

Originally Posted by ECO

There isn't anything here yet!

If you are interested in writing a tech summary, just post it below and I will rearrange the thread as appropriate.

Alternatively if anyone wants to post tech sheets, manuals, etc, I will write it. I just don't know enough of it beyond "pyrosequencing, picotiter plates, and a ton of beads".

gstitan · 01-20-2010, 03:29 AM

Does anybody already have to use CANGS? If yes he could explain to me why it filters primers sequences while this filter is already made by 454?

scrosby · 09-11-2011, 06:30 AM

With Illumina now going to 300bp, does there remain a viable role for 454?

pmiguel · 09-11-2011, 06:47 AM

Quote:

Originally Posted by scrosby

With Illumina now going to 300bp

link?

--
Phillip

scrosby · 09-11-2011, 06:58 AM

I should have said 'soon' going to to 150 PE. Before the end of the year, I believe?

pmiguel · 09-11-2011, 07:10 AM

Actually, with the results I saw from recent v3 runs I was wondering if anyone had pushed out past 100 nt on HiSeq chemistry already?

--
Phillip

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09-27-2008, 05:28 PM	#1
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Tech Summary: Roche's 454 GS20 / FLX / Titanium There isn't anything here yet! If you are interested in writing a tech summary, just post it below and I will rearrange the thread as appropriate. Alternatively if anyone wants to post tech sheets, manuals, etc, I will write it. I just don't know enough of it beyond "pyrosequencing, picotiter plates, and a ton of beads".

10-01-2008, 07:02 AM	#2
Tom Bair Member Location: Iowa Join Date: Oct 2008 Posts: 28	quick summary of titanium from 454 site Needed this for something else may be incomplete or wrong but .. 400-600 million high-quality, filter-passed bases per run 10 hours average length 400 bp more than 1x10^6 reads a cluster from roche is recommended for signal processing from www.pssclabs.com. It looks like image processing will still happen on the GS-FLX and 9G of cwf (wells) files need to go the the cluster from what I can tell it is a 5 node system (20 cores) the only specs I can find say redhat with either openMPI or MPI2 (mpiexec), SunGrid as scheduler runs will be 35GB (26GB images) A test data-set with a configuration tester is promised soon Rumor has it that bead breaking will be via centrifuge in the new protocol

06-10-2009, 03:29 PM	#7
SeqWhiskey Junior Member Location: Denver, CO Join Date: Jun 2009 Posts: 4	SV Look out for the SV prep on titanium. There is a pretty serious typo under the DNA capture step. 3.2.7 the volume to evenly distribute capture beads is off. It says 40ul per rxn, it's really more like 70+ul. In fact completely ignore this section and prep each rxn in individual 1.7ml tubes. The roche tech agrees with me... just wash with 3-400ul of cap bead wash buff so you don't run out.... Then again, does Ti even work as advertised?

01-20-2010, 03:29 AM	#9
gstitan Junior Member Location: Essonne Join Date: Oct 2009 Posts: 7	Cangs Does anybody already have to use CANGS? If yes he could explain to me why it filters primers sequences while this filter is already made by 454?

10-04-2008, 10:58 AM	#3
genseq Member Location: Russia Join Date: Dec 2007 Posts: 88	It isn't Titanium, but it is about new pyrosequencing from Illumina: Development of a 10Gb Pyrosequencer Ronaghi, Mostafa Illumina, Inc., San Diego, CA R01 HG003571 $5.1 million (3 years) Collaborators: Helmy Eltoukhy, Stevan Jovanovich (Microchip Biotechnologies, Inc.) We propose to develop a low-cost 10-Gb Pyrosequencer for de novo DNA sequencing that would enable any lab to perform high-throughput genome analyses. The platform implements automated sample preparation scheme combined with massive Pyrosequencing, which will potentially enable mammalian genome sequencing in a single run. A sensitive CMOS image sensor has been designed and fabricated specialized for Pyrosequencing chemistry, which is integrated with fluidic platform. Each well in the fluidic platform has a pixel on CMOS for detection of light signal generated from Pyrosequencing. The integrated chip will have a 2-megapixel CMOS, each pixel located on a single well enabling 2 million sequencing on each chip. Sixteen of such chips are set up on a board to develop a 32-million wells Pyrosequencer which potentially enable sequencing of more than 10 gigabase of genomic DNA. The raw data are immediately collected and assembled with our developed algorithms. We envision that the genome sequencing of mammalian genome to be reduced below $100,000 level for large-scale genome sequencing projects.

10-15-2008, 01:32 PM	#4
bioinfosm Senior Member Location: USA Join Date: Jan 2008 Posts: 482	I am confused by this .. "pyrosequencing from illumina" !

09-11-2011, 06:30 AM	#10
scrosby Director, GTAC, Washington U. Location: St. Louis Join Date: Nov 2009 Posts: 32	With Illumina now going to 300bp, does there remain a viable role for 454?

09-11-2011, 06:58 AM	#12
scrosby Director, GTAC, Washington U. Location: St. Louis Join Date: Nov 2009 Posts: 32	Forgive me... I should have said 'soon' going to to 150 PE. Before the end of the year, I believe?

09-11-2011, 07:10 AM	#13
pmiguel Senior Member Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008 Posts: 2,315	Actually, with the results I saw from recent v3 runs I was wondering if anyone had pushed out past 100 nt on HiSeq chemistry already? -- Phillip