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Old 03-20-2009, 07:49 AM   #1
Genomatix
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Location: Ann Arbor, MI

Join Date: Feb 2009
Posts: 12
Default First Post for New Vendor Forum

Hi Everyone!

This is a new forum dedicated to those of us who are interested in the science of NGS but who have a commercial affiliation...and want to talk about it. So if you are not interested in anything "commercial", then you probably don't what to be here.

We are from Genomatix, and have an extensive array of capabilities covering the entire continuum of NGS data analysis...from the raw sequence tag data mapping or assembly to a deep reach into the biology of the system of interest. We will be posting from time to time on things we have to offer the NGS community that we think/hope will be of interest. For the moment, let it suffice to say that there really is a "complete" solution for NGS data analysis...and we have it.

More to come....
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Old 03-27-2009, 07:51 AM   #2
Genomatix
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Default "Complete" solution?

I'd like to take a moment to respond to a comment (which I believe is a widely held view) from the CHI NGS conference thread that no one out here has a "comprehensive" solution for NGS data analysis.

Since this is a vendor forum, I'm going to take the liberty of saying that Genomatix does indeed have a comprehensive (in fact, turnkey) solution for NGS data analysis, starting from the tag sequence information from any of the 4 current platform vendors. We provide graphical user interface or command line access to map to a reference, assemble without a reference, do de novo SNP analysis (homo or heterozygous),
CNV analysis, or a splice junction analysis by mapping against our own splice junction library. We can also provide an automated analysis of your "interesting" sequences (as defined by your NGS data) in search of putative new transcription factor binding sites, and compare them to existing ones already defined in our library.

Reaching from there deeper into the biology, we provide application specific analysis (still with either a GUI or command line access) for common applications like RNA-Seq or ChIP-Seq experiments, such as orthologous searches of sequences of interest across our extensively annotated genome data base (19 species), over-represented TFBSs, expression values, and extensive capabilities for meta-data analysis.

We will continue to expand our capabilities to keep pace with the explosion of applications that continue to flow from this exciting technology.

Thanks for reading!
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Old 03-27-2009, 10:45 AM   #3
Chipper
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Location: Sweden

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Looks like a good package, but who can afford it?...
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Old 04-09-2009, 12:07 PM   #4
Genomatix
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Location: Ann Arbor, MI

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Default Who Can Afford It

I'd like to suggest a different question...who CAN'T afford it! Doesn't matter whether you're from an academic or commercial institution, you will spend upwards of $500,000 (or more) for your NGS machine...a machine that is entirely capable of burying you in data in a very short time. My question is, does it make sense to stitch together multiple "pieces" of software (commercial and/or freeware) that come from widely varying sources...some much better than others...and struggle trying to build an analysis pipeline that can keep pace with the data output, or does it make sense to spend additional money for an integrated, complete capability that will allow you to build multiple analysis pipelines that will easily keep pace with your analyzer? There are way too many labs out there that have slowed their data production down so that they can catch up with the data. Seems to me to be wasting money spent on a high throughput instrument if you can't run it at full capacity?

Our package is certainly not for everyone, but I hope if you're considering an NGS machine purchase, that you will additionally consider the cost of making sense of all the data it will generate. Biological sense, that is. Ultimately, that's what these machines are all about...being able to dig deeper/faster into the biology of your system of interest. Don't cut yourself short!

Thanks for reading!
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