New PacBio system: Sequel

[GenoMax]

Originally Posted by Brian Bushnell

Both! I left Google and came back to JGI. So, it's at JGI.

Google's loss but good for us

We will have to count on you @Brian to see some unbiased eval of Sequel data once you get your hands on some.

[luc]

Originally Posted by GenoMax

Google's loss but good for us

Ditto!


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[spore]

Does anyone have information on how the Sequel data compares to the RSII? And when service providers will begin offering Sequel services?

[GenoMax]

It is hard to tell but the description for this dataset seems to include verbiage about Sequel (not sure why the submitters would include that if this was a RSII): http://www.ebi.ac.uk/ena/data/view/SRX1684788

Most likely a red herring but who knows. Raw bax/bas.h5 files are available in case someone is curious (http://trace.ncbi.nlm.nih.gov/Traces...run=SRR3342814 under Download tab).

[sajeshpk]

Originally Posted by Brian Bushnell

No... most of what we sequence comes from remote users. But, we do all the library construction here, and I believe we reject samples that do not have high molecular weight DNA, or insufficient mass.

Hi
We are facing some issues with our new sequal system installed recently. Pacbio team is unable suggest loading clear loading concentration of different sized library.
The out put varies with each run and the maximum we got till now is 3.2gb for 2 kb library.
For the higher sized library the runs will yield 0.2-0.9gb per SMRT.We are unable to find out where the problem lies.Also after completing each run the volume of libraries pickedup from the sample well is not consistent.
Pac bio suggestion for the loading conc is 50-60pM for any size library.

There is another suggestion from PacBio is that system and smrtlink need to be restarted every 24 days, Is it true?

Please help

[nucacidhunter]

Originally Posted by sajeshpk

Hi
We are facing some issues with our new sequal system installed recently. Pacbio team is unable suggest loading clear loading concentration of different sized library.
The out put varies with each run and the maximum we got till now is 3.2gb for 2 kb library.
For the higher sized library the runs will yield 0.2-0.9gb per SMRT.We are unable to find out where the problem lies.Also after completing each run the volume of libraries pickedup from the sample well is not consistent.
Pac bio suggestion for the loading conc is 50-60pM for any size library.

There is another suggestion from PacBio is that system and smrtlink need to be restarted every 24 days, Is it true?

Please help

I wonder if this is about recently released chemistry and software (December release) or previous one releaed October this year.

[sajeshpk]

Hi
The reagent version is 1.2.1 and software is SMRT Link UI 3.1.1
Change 182734 on 2016/07/07
Sajesh

[GenoMax]

Originally Posted by sajeshpk

There is another suggestion from PacBio is that system and smrtlink need to be restarted every 24 days, Is it true?

Please help

Welcome to the (somewhat) wacky world of PacBio.

I would suggest following all recommendations from PacBio/your FAS and keeping a good log of everything to help with troubleshooting.

A brand new technology/system needs to undergo a shakedown in real user's hands and perhaps this is just part of that process.

[luc]

Further, single-molecule sequencing has lots of variables related to sample quality and sample handling. I would suggest to start with a libraries prepped from "easy and reproducible " samples like amplicons.

[sajeshpk]

Thanks Friends
Sajesh

[AllSeq]

For those who may have missed it - Roche Diagnostics pulled out of their marketing agreement with PacBio: http://www.pacb.com/press_releases/p...e-diagnostics/. In the short term this means PacBio stock is cratering. In the mid- to long-term it means PacBio will have to (or 'gets to', depending on your perspective) bring a clinical version of the Sequel to market.

[sundew]

does anybody know what service price per cell will be? is somebody who already offer service on Sequel?

[pacbio]

Here is a list of PacBio certified service providers, including those who offer services on the Sequel System: http://www.pacb.com/wp-content/uploa..._Providers.pdf

[nucacidhunter]

I wonder if you could post a separate list for Sequel service providers.

[sajeshpk]

Originally Posted by nucacidhunter

I wonder if you could post a separate list for Sequel service providers.

Hi
Pls send the details on sajeshpk@aggenome.com.We are providing sequel services

[Sandra Agueros]

Does anybody knows how much a Pac Bio run take up in Gigabytes storage?
For example, a NextSeq Run can take up to 1.2 Tb in storage. I need this info pleaasee! jeje Thanks

[gringer]

From what I've been told, really good PacBio runs produce about 10Gb of sequence data. I would expect that PacBio will produce less raw data than nanopore for the same sequence output, so I expect that you should be fine with about ten times that amount in space to store both sequence and raw data (i.e. 100GB).

[GenoMax]

Originally Posted by Sandra Agueros

Does anybody knows how much a Pac Bio run take up in Gigabytes storage?
For example, a NextSeq Run can take up to 1.2 Tb in storage. I need this info pleaasee! jeje Thanks

We just received some Sequel data and the size of the tar files was about 20G for each cell. From past experience RSII data was ~15-25G per SMRTcell (uncompressed).

[SanDiegome]

Originally Posted by nucacidhunter

I wonder if you could post a separate list for Sequel service providers.

A bit late to the party, but you can find a list of Sequel providers on AllSeq.

--Shawn

[BioKiwi]

We have found Sequel output to be inconsistent and not sure if it is our machine. Just completed three SMRT cell runs with one library prepared for sequencing in bulk sequenced one after another but the output varies up to 125% ( 4.5, 2 and 3Gb output). I wonder if anyone have seen similar results.