Companies offering next gen sequence analysis services

gavin.oliver · 01-08-2010, 08:40 AM

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

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

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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01-08-2010, 08:40 AM	#1
gavin.oliver Senior Member Location: uk Join Date: Jan 2010 Posts: 110	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 Gavin

01-08-2010, 10:57 AM	#2
apfejes Senior Member Location: Oakland, California Join Date: Feb 2008 Posts: 236	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. __________________ The more you know, the more you know you don't know. —Aristotle

01-10-2010, 05:10 PM	#3
ScottC Senior Member Location: Monash University, Melbourne, Australia. Join Date: Jan 2008 Posts: 246	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.

01-10-2010, 05:25 PM	#4
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Go for it, or I can move this one to the Service Providers forum.

01-11-2010, 12:42 AM	#5
gavin.oliver Senior Member Location: uk Join Date: Jan 2010 Posts: 110	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?

01-11-2010, 03:16 AM	#6
steven Senior Member Location: Southern France Join Date: Aug 2009 Posts: 269	I totally agree: a specific list for analysis services (from academia, companies, sequencing centers..) would be definitely more than useful!

01-12-2010, 01:19 AM	#7
gavin.oliver Senior Member Location: uk Join Date: Jan 2010 Posts: 110	Any volunteers or alternatively suggestions on how to go about creating this list? As it stands I wouldn't know where to start.

01-12-2010, 03:48 AM	#8
steven Senior Member Location: Southern France Join Date: Aug 2009 Posts: 269	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.