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-   -   Companies offering next gen sequence analysis services (http://seqanswers.com/forums/showthread.php?t=3566)

gavin.oliver 01-08-2010 08:40 AM

Companies offering next gen sequence analysis services
 
Hi all,

I am new to this field and am currently doing some background research. I'm just wondering initially if there are many (any?) companies out there who offer next gen sequence analysis services?

Thanks in advance :D

Gavin

apfejes 01-08-2010 10:57 AM

Several sequencing centres do (including the one where I'm currently studying). However, you might want to specify which technology you're looking for, as it may make a difference in terms of what people suggest for you.

ScottC 01-10-2010 05:10 PM

Yes, as apfejes mentioned, there are plenty of companies that provide a range of services for next gen sequencing and analysis... also including ours :-)

Have you seen this list? I know it's not listing analysis services alone, but I think there will be many in there that can do it.

http://seqanswers.com/forums/showthread.php?t=948

Maybe we should start a second list for analysis services...

Scott.

ECO 01-10-2010 05:25 PM

Go for it, or I can move this one to the Service Providers forum. :)

gavin.oliver 01-11-2010 12:42 AM

Thnaks for the replies!

From my perspective, a separate list for analysis services would be useful but I don't know what other members' opinions are?

steven 01-11-2010 03:16 AM

I totally agree: a specific list for analysis services (from academia, companies, sequencing centers..) would be definitely more than useful!

gavin.oliver 01-12-2010 01:19 AM

Any volunteers or alternatively suggestions on how to go about creating this list? As it stands I wouldn't know where to start.

steven 01-12-2010 03:48 AM

Potentially interesting info could be:

Name of the analysis tool
URL
Source: company name, institute
Price: free or $oft
Supported machines (platform)
OS: Linux, Mac, Windows, public web based platform..
GUI: none (command line), yes, web-based, with genome browser..
Input: raw image, fastq reads, alignment files, BED files..
Output: numbers, tables, graphs, Excel sheets..
Ref (papers, if any)
Base calling: Y/N + method
Read alignment: Y/N + method
Read assembly: Y/N + method
SNP calling: N/Y + method
Genomic variations, etc: Y/N + method
Gene expression: Y/N + method (RPKM, etc)
Other features

Thoughts, comments? Anybody else interested?
Additional suggestions before starting the table? (a new thread in the service providers section i guess?)
s.

krobison 01-12-2010 05:27 AM

Quote:

Originally Posted by steven (Post 12264)
Potentially interesting info could be:

Name of the analysis tool
URL
Source: company name, institute
Price: free or $oft
Supported machines (platform)
OS: Linux, Mac, Windows, public web based platform..
GUI: none (command line), yes, web-based, with genome browser..
Input: raw image, fastq reads, alignment files, BED files..
Output: numbers, tables, graphs, Excel sheets..
Ref (papers, if any)
Base calling: Y/N + method
Read alignment: Y/N + method
Read assembly: Y/N + method
SNP calling: N/Y + method
Genomic variations, etc: Y/N + method
Gene expression: Y/N + method (RPKM, etc)
Other features

Thoughts, comments? Anybody else interested?
Additional suggestions before starting the table? (a new thread in the service providers section i guess?)
s.

Much of what you quote below is what is in the software Wiki. A separate Wiki for paid sequencing & analysis services could be useful, but duplicative effort should be minimized. I would lump actual sequence production with software services; many organizations offer both (either directly or as a pass-through).

For example, if something is a service then the OS & GUI seem pretty irrelevant questions. Perhaps you do want to include free services, but then only the web-based ones and not anything that requires installation locally beyond getting the right common accessories (Java runtime, Flash, etc)

If as a Wiki, rather than a bunch of Y/N it would probably make more sense to have a compact (but expandable) set of keywords with agreed meaning. Those might be in larger categories (again, the software Wiki is a good model to start with).


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