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Old 04-06-2010, 07:24 AM   #1
msincan
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Default turn-key next gen companies

I have been trying to ride the next gen sequencing tsunami for some time now. To the best of my understanding the sequencing technology is getting to a point where it is very rapidly becoming a commodity. What you do with the data once the raw sequencing data is spit out by the sequencing machines is still a bigger question in my mind. So I think any sequencing service is not complete unless the data cleaned, curated and analyzed to a minimum degree. I mean alignment and genotype and variation determination. So if you are not fortunate enough to be in one of the world excellence centers like the broad institute what are your options in terms of commercial companies that get your samples and give you a list of variants for that sample. This is similar to a clinical lab giving you the meaningful results that can be interpreted clinically compared to the raw chromatogram images that the biochemical analyzer generates. Any thoughts?
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Old 04-06-2010, 08:09 AM   #2
dgaalaas
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Hello msincan-

I am not convinced next-gen sequencing is becoming a commodity at a rapid pace. You can find wild swings in terms of data amount, accuracy of data and quality of data from lab to lab, much more so then you can currently find in CE sequencing. However, many commercial service providers are starting to add a bioinformatics capability, although at a very basic level when compared with places like the Broad and WashU. It depends on how much curation of the data one needs. I represent a service provider so I do not want to get into specifics in this space as it would be inappropriate. If interested please tweet me at @dgaalaas.
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Old 04-06-2010, 08:58 AM   #3
msincan
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What I mean by next gen sequencing becoming a commodity is that the cost and time required to run the reactions to determine a base is becoming so little. But as I point out I do believe the challenge is still there in terms of coming up with a reliable and complete solution to give not just the sequence but the real information that comes out from analyzing the sequence.
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Old 04-06-2010, 09:48 AM   #4
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Yes, the data analysis is the rate limiting step at this point.

There are only two commercial turn-key software analysis packages that I am aware of
CLC Bio's Genomic Workbench and NextGene from Softgenetics.

However, even after you analyze your data (assemble and determine variants), the next difficult step is determining the significance of those variants. This is not trivial since there are so many.
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Old 04-06-2010, 11:29 AM   #5
msincan
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Thanks NextGenSeq this is exactly the kind of discussion I was hoping to get. When you say determine the significance are you referring to methods such a s SIFT and PolyPhen or are you going one step further and talking about if the variant that has been ranked as a deleterious variant is actually causing the disease or having a significant biological/functional effect?
I think may be galaxy may evolve into its next version that may be a viable alternative to commercial products or I am also very interested in hearing about cloud computing based solutions.
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Old 08-11-2010, 08:30 AM   #6
mgabrielli@partek.com
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There's also Partek - give it a try at www.partek.com...
Really, in looking for a complete solution, Partek is the software to use.

Taking RNA-Seq, Ch-IP-Seq, DNA-Seq, Methyl-Seq data from alignment, to Quality Control, to Statistical Analysis, to Biological Analysis and also to Functional Genomics by correlating data across assays -> you get a complete picture for your biological hypothesis.

I agree the fun begins with the biological/functional effect, the visualizations in Partek report this nicely.
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Old 08-11-2010, 12:05 PM   #7
Zigster
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how much does a Partek subscription cost a year? $7 million?! That can't be right.

https://www.fbo.gov/index?s=opportun...=core&_cview=0
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Old 08-11-2010, 02:49 PM   #8
mgabrielli@partek.com
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Ha! That's a good one!
Partek is the most affordable commercial genomics sw to my knowledge.
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Old 08-11-2010, 11:33 PM   #9
strob
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Hi,

if you sequence your data with BGI, the bioinformatics analysis are included. And from our experience they are not only with many people, they also provide really nice curated data (even on difficult plant genomes). You can read an example in this press release: http://www.bayercropscience.com/bcsw...25764A002DE77C
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