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Convert Solid BAM/SAM to Solid GFF? ioannis Bioinformatics 0 07-20-2010 08:06 AM

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Old 10-24-2010, 06:59 PM   #21
KevinLam
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Oh there was a brief mention of the Ion Torrent at the presentation as well but nothing of great significance. I do wish they marketing fellows will push ion torrent out faster but i think they are trying to streamline production by testing if invitrogen kits can replace the ones at ion torrent. I do hope they do not sacrifice compatibility over performance
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Old 10-25-2010, 12:04 AM   #22
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regarding "performance of Ion Torrent" in that seminar they´ve also mentioned that the accuracy of the PGM is increasing and could reach q40 at launch (e.coli; ~2-6x coverage).
In terms of speed one can go for up to 4 runs per day.
Application number will increase too because of the R&D-man-power behind LifeTech compared to Ion Torrents.
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Old 10-28-2010, 10:57 PM   #23
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Default SOLiD @ ASHG

AB is premiering two new instruments at ASHG next week.

Mobile ASHG calendar: http://m.appliedbiosystems.com/ashg/

Twitter account: @SOLiDSequencing

SOLiD Community: http://solid.community.appliedbiosystems.com/

More info soon at: solid.appliedbiosystems.com/solid5500/

Last edited by truthseqr; 10-28-2010 at 11:21 PM.
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Old 11-01-2010, 04:21 PM   #24
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Looks promising. Up to 230 M fragments per lane and possibility to run 1 lane in one day.

* Pay-per-use reagents for cost-effective
consumable usage

* 1 day for 35 bp, 1 lane

* Nanobeads: Up to 300 Gb or greater than 4.8 B tags (paired-end or
mate-paired runs)

* Reference-free analysis with Exact Call Chemistry Module
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Old 11-03-2010, 06:39 AM   #25
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From the In Sequence article, link, but login is required:

"Real-time data processing means no compute cluster is necessary."

Any idea how this could be possible when a cluster is required to run a solid v4 and it does data processing on the fly, if not exactly "in real time"?

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Old 11-03-2010, 08:21 AM   #26
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Quote:
Originally Posted by pmiguel View Post
From the In Sequence article, link, but login is required:

"Real-time data processing means no compute cluster is necessary."

Any idea how this could be possible when a cluster is required to run a solid v4 and it does data processing on the fly, if not exactly "in real time"?

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I recall speculation that V4 to HQ cannot be upgraded as its entirely different.
In the preview launch they did allude to the fact that instead of slides it is now 6 lanes of microfluidic on a flowchip (which still looks like a slide to me though)

and the highly advertised fact that "Developed and manufactured with long-standing partner Hitachi High-Technologies, the 5500xl delivers on the promise of the SOLiD 4hq"

So based on this I am guessing the optics and fluidics are changed. Hence perhaps that's the main reason behind not requiring a on instrument cluster.

however, if you asked me, I really feel that the cluster was provisioned so that users may run at least bare minimal analysis on the data, without having to buy an offline cluster. The running time of the cycle scans are probably long enough to process the images with a desktop computer. granted it has enough storage.

just my two cents.
btw for those that do not have access to genomeweb try the official press release.
http://www.lifetechnologies.com/news...aces-i--c.html
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Old 11-03-2010, 08:30 AM   #27
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Specs for 5500 and 5500xl.
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Old 11-03-2010, 08:45 AM   #28
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@Kevin
Is it possible they follow the illumina way? To use a powerful machine for the
image processing and base calling. They don't mention details of the onboard
machine, other than runs windows.

Notice how in the brochure (thanks ECO) saids that the ECC feature requires a module.
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Old 11-03-2010, 08:50 AM   #29
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We actually had occasion to repeat image analysis on a completed run of one full slide (~500 million usable beads). (This is not "primary analysis", that occurs after image analysis.) The instrument was otherwise idle. Our solid v4 linux cluster was pegged at 100% load on all 4 nodes for the duration. It took about 1.5 hours/base processed. That is >5 days of wall clock time for a run that completed in about 2 weeks. So that works out to about 40% of the capacity of the cluster had the full 2 weeks to run. Since the solid has 2 flowcells, it might be called upon to do image processing on the fly for both at the same time.

This suggests that the cluster is slightly over provisioned ( by about 25%).

The 5500xl has 2 flowcells like the v4 and will have to process more beads. So no relief there for our console computer.

Perhaps the computation becomes simpler because a sample will be divided across 6 discrete lanes per flow cell? But it seems more likely there has been some break through in the process that has drastically reduced the computational resources required to do image processing.

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Old 11-03-2010, 09:37 AM   #30
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ECC module means that you run a 6th primer that gives you direct basespace output. Has nothing to do with any additional hardware.
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Old 11-03-2010, 12:59 PM   #31
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Is there any documentation about ECC?
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Old 01-20-2011, 04:13 AM   #32
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Any ideas on real release dates for the 5500XL (solid 4hq) ? Has anyone got one yet ?

"Initial shipments of the 5500xl are planned for December 2010."

Oh that was from the press release at
http://www.lifetechnologies.com/news...aces-i--c.html

Last edited by colindaven; 01-20-2011 at 04:13 AM. Reason: add
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Old 01-20-2011, 05:21 AM   #33
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Rumours I have heard is march 2010. Not sure what's the hold up.
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Old 01-20-2011, 05:52 AM   #34
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There may be 5500xls in the field, if only as test units. That would fulfill the "initial shipments" claim.

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Old 01-21-2011, 02:15 AM   #35
Enrico Palazzo
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Yes, release date is March/2011. Does anybody know the new output format? I believe it is called XSV or something like this..
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Old 01-24-2011, 10:12 AM   #36
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Quote:
Originally Posted by Enrico Palazzo View Post
Yes, release date is March/2011. Does anybody know the new output format? I believe it is called XSV or something like this..
I believe it is called HDF, which is a standardized file format (single file replaces csfasta, qual, and spch files).
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Old 01-25-2011, 03:15 PM   #37
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At the Sequencing at the Tipping Point Conference, back in December, they were saying the new file format would be .xqs (or maybe it was .xsq?)
Its a binary file format, with one file per lane. This is supposed to be why theres no need for a cluster under the machine, its like 60% smaller.
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Old 01-25-2011, 05:03 PM   #38
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Sorry, just remind me. It is called .xsq (eXtensible SeQuence)
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Old 01-26-2011, 05:49 AM   #39
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I think the reason for not having a minicluster is the use of FPGAs along with a very powerful machine (like illumina). Anyone has more info about that? I guess we'll find out at AGBT.
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Old 01-26-2011, 09:37 AM   #40
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Yes, I have ".xsq" in my notes as the new format name. They were going to be about 30 gigabytes per lane. 12 lanes per "flow chip".

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