Software packages for next gen sequence analysis - Page 12

ECO · 11-13-2009, 07:12 AM

Quote:

Originally Posted by wuhoucdc

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, 09:30 AM

Thanks ECO for your kind suggestions.

Wuhoucdc

Y.Y. LEUNG · 11-15-2009, 06:58 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, 07:03 PM

Quote:

Originally Posted by 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.

I am tempted to push you toward cygwin.

apfejes · 11-15-2009, 07:05 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, 07:30 PM

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

Marta · 11-16-2009, 08:38 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 · 11-16-2009, 11:12 PM

Quote:

Originally Posted by 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

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, 05:26 AM

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

Stegger · 11-17-2009, 11:05 PM

Their 36 bases.

dan · 11-19-2009, 06:57 AM

Quote:

Originally Posted by ECO

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

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, 07:03 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, 08:20 PM

Quote:

Originally Posted by 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?

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, 12:22 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, 05:59 PM

good thing thanks

hanjaylee · 12-25-2009, 05:40 PM

nice work!

ECO · 12-25-2009, 05:45 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.

11-15-2009, 07:05 PM	#225
apfejes Senior Member Join Date: Feb 2008 Location: Vancouver, Canada Posts: 220	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. __________________ The more you know, the more you know you don't know. —Aristotle

12-11-2009, 12:22 AM	#234
dan Wiki Master Join Date: Jul 2008 Location: Dundee, Scotland Posts: 94	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. __________________ Homepage: Dan Bolser MetaBase the database of biological databases.

11-13-2009, 09:30 AM	#222
wuhoucdc Member Join Date: Oct 2009 Location: Nashville Posts: 14	Thanks ECO for your kind suggestions. Wuhoucdc

11-15-2009, 06:58 PM	#223
Y.Y. LEUNG Junior Member Join Date: Sep 2009 Location: HK Posts: 6	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.

11-15-2009, 07:30 PM	#226
ScottC Senior Member Join Date: Jan 2008 Location: Monash University, Melbourne, Australia. Posts: 125	There's also CLC Genomics Workbench (although it is a commercial package).

11-16-2009, 08:38 PM	#227
Marta Member Join Date: Oct 2009 Location: Davis, CA Posts: 14	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

11-17-2009, 05:26 AM	#229
Marta Member Join Date: Oct 2009 Location: Davis, CA Posts: 14	Stegger, thanks! Is is nice to know that CLC Workbench can run on a 3GB machine. How long are your 10M reads?

11-17-2009, 11:05 PM	#230
Stegger Member Join Date: Nov 2008 Location: Copenhagen Posts: 15	Their 36 bases.

12-10-2009, 07:03 PM	#232
Nomijill Member Join Date: Sep 2009 Location: Southwest Florida Posts: 15	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?

12-22-2009, 05:59 PM	#235
lvxiaobao Junior Member Join Date: Oct 2009 Location: guangzhou city ,guangdong province ,china Posts: 6	good thing thanks

12-25-2009, 05:40 PM	#236
hanjaylee Member Join Date: Dec 2009 Location: china Posts: 10	nice work!

12-25-2009, 05:45 PM	#237
ECO --Site Admin-- Join Date: Oct 2007 Location: SF Bay Area, CA, USA Posts: 660	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.