Software packages for next gen sequence analysis

[ECO]

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.

[hanjaylee]

nice work!

[lvxiaobao]

good thing thanks

[dan]

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.

[ECO]

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!

[Nomijill]

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?

[dan]

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!

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:BrowseData/Bioinformatics%20application?Biological_domain=Structural_variants

;-)

[Stegger]

Their 36 bases.

[Marta]

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

[Stegger]

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]

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

[ScottC]

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

[apfejes]

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.

[nilshomer]

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.

[Y.Y. LEUNG]

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.