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

[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".

[Tom Bair]

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

[bioinfosm]

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

[monad]

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]

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.

They bought Avantome.

[SeqWhiskey]

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?

[edge]

Hi,

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

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]

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?

[scrosby]

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

[pmiguel]

With Illumina now going to 300bp

link?

--
Phillip

[scrosby]

Forgive me...

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

[pmiguel]

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