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Old 10-07-2012, 05:05 PM   #1
slny
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Default commercial software in sequencing analysis

Hi,

I just got some funding to purchase commercial software for next generation sequencing data analysis, but I'm very new in sequencing analysis.

Could anyone give me a list of the commonly used commercial software?

Thanks a lot in advance!
slny
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Old 10-08-2012, 03:41 AM   #2
severin
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Default Informatics core facility

I feel you are better off spending the funding with a local core bioinformatics facility that is willing to train you with the skills to use open source software. This field is changing so rapidly that the analysis you do this year will require a completely new software bundle in 4 months. Many of the commercial software out there can be as high as $5,000 a year! You can get a lot of training and data analyzed for that amount of money. Commercial software are usually black box that do specific tasks that may or may not be what you need for your specific biological question of interest.

Open source solutions
Need an alignment done? GSNAP
Need it done fast? SOAP3-dp
Need SNPS/InDels? GATK
RNA-Seq? Diff Exp? Quasi-Seq, DESeq, DEXSeq, EdgeR, cuffDiff?
Filtering reads? ShortRead, Fastxtoolkit
Genome Assembly AllPaths-LG, Velvet, Ray, Soap-Denovo,
Transcriptome assembly Velvet/Oases, Soap-DenovoTrans, Ray,
Metagenomics Meta-Velvet
And it goes on and on.




**This may be biased since I run a core facility but I wouldn't be doing what I love if I didn't believe it was the way to go**
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Old 10-08-2012, 04:36 AM   #3
GenoMax
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I fully agree with severin's comments,

but it is possible that

a) slny does not have access to a local bioinformatics core that can be called/relied upon
b) if there is a core available it may be understaffed and/or not responsive to needs of a small PI/single user
c) funding slny acquired may need to be used for the specific purpose of buying software
d) not every one is comfortable working on the command line/have access to necessary compute infrastructure

slny: A comprehensive list of various software packages can be found here: http://seqanswers.com/wiki/Software/list The list includes both commercial and free software.

Most software vendors will provide some sort of trial license so you should compare and contrast the packages and decide what works best in your specific case.

Before you go down the path of commercial software take into consideration the annual expense of a maintenance contract that may be required to receive continued updates/tech support. Depending on how the licensing for the package you choose works, you could lose access to your own data/analysis if you let the license for the software expire.
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Old 10-08-2012, 06:25 AM   #4
zee
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It is most likely that one piece of software is not going to bring it all together. You will need some help integrating and maintaining a very good pipeline(s) for processing sequence data.

For reference based work start with a good sequence aligner, it will form the base for generating good quality results that work downstream. Severin mentioned some good options however not all of those are available free for commercial use. We develop the novoalign (www.novocraft.com) aligner which is also quite popular. It is a 'commercial' software and it's free to explore without purchasing.
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Old 10-08-2012, 01:30 PM   #5
swNGS
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It depends a lot on what you want to do, could you give a bit more detail please?
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Old 10-11-2012, 05:51 AM   #6
david2
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slny,

it would help to know your background (biology? Expertise in IT?Linux?) and your applications of NGS (target resequencing? WES? de-novo?RNA-Seq?...) What's the profile of the person who will have to use the tool (if not yourself)?

The above mentioned list is quite complete, you will just need some time to try out the many options.
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Old 10-11-2012, 06:14 AM   #7
mbblack
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Quote:
Originally Posted by slny View Post
Hi,

I just got some funding to purchase commercial software for next generation sequencing data analysis, but I'm very new in sequencing analysis.

Could anyone give me a list of the commonly used commercial software?

Thanks a lot in advance!
slny
In case you are not aware, most such software cannot be purchased, it is usually licensed with an annual contract fee (Partek, JMP Genomics, CLC Bio Workbench, and others). The cost of a contract will depend on a number of things (e.g. do you need remote access? how many users? which modules for some that are broken out by such?).

SeqAnswers also has a software Wiki - http://seqanswers.com/wiki/Software

I'd suggest looking through that as well.

Most commercial software vendors will also set you up with a trial license if you ask them, so you can evaluate their software directly. So if you see something you think you might want, you can check it out before paying for a full contract period.
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Last edited by mbblack; 10-11-2012 at 06:17 AM.
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Old 10-13-2012, 08:57 AM   #8
slny
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Hi Everyone,

Thank you very much for all the responses. The information is very complete. I sincerely appreciate all the help!

Best,
slny
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