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-   -   Software packages for next gen sequence analysis (http://seqanswers.com/forums/showthread.php?t=43)

ECO 11-13-2009 08:12 AM

Quote:

Originally Posted by wuhoucdc (Post 10423)
Hi all,

Who have the time to summarize the programs that can be used call SV such as large rearrangement, deletion, amplication among NGS? Thanks.

Wuhoucdc

You are more than welcome to start annotating the software packages in our wiki: http://wiki.seqanswers.com. I believe Dan is working on a set of instructions for new wiki users.

Thanks!

wuhoucdc 11-13-2009 10:30 AM

Thanks ECO for your kind suggestions.

Wuhoucdc

Y.Y. LEUNG 11-15-2009 07:58 PM

Seems that most of the softwares are available in Linux environment.

Are there any softwares recommended for use in Windows for RNA-seq or targeted sequencing projects? the data are obtained from Solexa, 454 and SoLID.

Thanks for your help.

nilshomer 11-15-2009 08:03 PM

Quote:

Originally Posted by Y.Y. LEUNG (Post 10451)
Seems that most of the softwares are available in Linux environment.

Are there any softwares recommended for use in Windows for RNA-seq or targeted sequencing projects? the data are obtained from Solexa, 454 and SoLID.

Thanks for your help.

I am tempted to push you toward cygwin.

apfejes 11-15-2009 08:05 PM

Depends what you're trying to do - I've used Vancouver Short Read Analysis Package/FindPeaks (my own software) for RNA-Seq (alternative exon expression) and had good luck - I don't use it in windows, myself, but java is cross-platform and I know people have successfully used in that environment.

ScottC 11-15-2009 08:30 PM

There's also CLC Genomics Workbench (although it is a commercial package).

Marta 11-16-2009 09:38 PM

Yes, CLC Genomics Workbench will use all three data types. I use the program on Windows. However you will need lots of RAM. For my files/genomes I needed 32GB (the max we could put into my box). If you work with small bacterial genomes and simple transcriptomes you maybe able get away with 8GB RAM (the minimal requirement for CLC Workbench)

Marta

Stegger 11-17-2009 12:12 AM

Quote:

Originally Posted by Marta (Post 10510)
Yes, CLC Genomics Workbench will use all three data types. I use the program on Windows. However you will need lots of RAM. For my files/genomes I needed 32GB (the max we could put into my box). If you work with small bacterial genomes and simple transcriptomes you maybe able get away with 8GB RAM (the minimal requirement for CLC Workbench)

Marta

I am using the CLC Genomics Workbench on my laptop running XP with 3 GB and it handle up to about 10 million Illumina reads in a de novo assembly, but things larger than that causes problems on my small machine. So it seems you can work with smaller bacterial genomes on less than 8 GB of ram, at least that is my experience.

Marta 11-17-2009 06:26 AM

Stegger, thanks! Is is nice to know that CLC Workbench can run on a 3GB machine. How long are your 10M reads?

Stegger 11-18-2009 12:05 AM

Their 36 bases.

dan 11-19-2009 07:57 AM

Quote:

Originally Posted by ECO (Post 10424)
You are more than welcome to start annotating the software packages in our wiki: http://wiki.seqanswers.com. I believe Dan is working on a set of instructions for new wiki users.

Thanks!

Quote:

Originally Posted by wuhoucdc (Post 10423)
Hi all,

Who have the time to summarize the programs that can be used call SV such as large rearrangement, deletion, amplication among NGS? Thanks.

Wuhoucdc

Just click here:

http://seqanswers.com/wiki/Special:B...tural_variants


;-)

Nomijill 12-10-2009 08:03 PM

Sciguy, I notice that you last updated your list in August. Are there any significant changes since then? Or am I wrong about the reading of the update?

ECO 12-10-2009 09:20 PM

Quote:

Originally Posted by Nomijill (Post 11383)
Sciguy, I notice that you last updated your list in August. Are there any significant changes since then? Or am I wrong about the reading of the update?

It's definitely been updated since...when I use my superpowers to edit the first post, it doesn't show the date.

The data @ http://wiki.seqanswers.com is probably a bit more current as it's being maintained by the community rather than just sciguy and myself!

dan 12-11-2009 01:22 AM

I'm guessing we need some kind of wiki forum ... but I not sure what form... um?

I think the problem is that the wiki is so bad for threaded conversations, we need a place to discuss the wiki...

For each software package that is in the wiki, I have added a link to search the forum for that package. This is only a small step. Generally I'm not sure how to more tightly integrate the two different approaches.

lvxiaobao 12-22-2009 06:59 PM

good thing thanks

hanjaylee 12-25-2009 06:40 PM

nice work!

ECO 12-25-2009 06:45 PM

Locking this thread for now, as the wiki is easier to maintain and this thread seems to have outlived its usefulness.

If you have a question about a specific package...and have already searched for the answer, please start a new thread about it.


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