SequenceVariantAnalyzer: analyzing genetic variants from next-gen sequencing

Dongliang Ge · 11-25-2009, 06:31 AM

Friends,

If you are working on next-generation sequencing studies, particularly if you are interested in annotating, visualizing SNPs, INDELs, CNVs, and identifying genetic variants responsible for biological traits or diseases, please check out our software tool SequenceVariantAnalyzer (SVA):

http://www.svaproject.org/

SVA is designed for two specific aims:

To annotate the biological functions of the identified genetic variants, organize and visualize them;
To help find the genetic variants that are associated with or responsible for the biological traits or medical outcomes of interest.

The SVA release package comes with an example project extracted from 10 genomes - 5 cases and 5 controls. To reduce the size of the release package, I release only the data on chromosome X. The web page below shows that you can play with SVA and an example project to "identify (again )" the Factor VIII (F8) gene for type A hemophilia:

http://www.svaproject.org/fastrun.php

SVA is also featured with an integrated genome browser to help an investigator to explore the user-generated data and data from public domains. Here is a screenshot:

http://www.svaproject.org/screenshot1.php

Particularly, SVA genome browser allows you to conveniently 'introduce' key variants that you identified to compare and see the difference they could make.

Please give it a try and let us know what you think.

Lastly, I hope you may find this tool helpful for your next-generation discovery!

Best regards,

Dongliang Ge,
Duke University, USA
http://people.genome.duke.edu/~dg48/

Dongliang Ge · 01-23-2010, 05:07 PM

SVA is just released!

Check it out at: http://www.svaproject.org/

Dongliang Ge · 01-23-2010, 05:08 PM

Its wiki page:

http://seqanswers.com/wiki/SequenceVariantAnalyzer

NGSfan · 02-08-2010, 05:15 AM

Thanks! Looks interesting! I will have a try with it.

Dongliang Ge · 02-11-2010, 02:20 PM

SVA comes with two editions:
1. Standard edition : ~2.2 Gb. This edition has full annotation functions.
2. Lite Evaluation edition: ~ 250Mb. This edition does not have annotation function, but can be used to load an example project for evaluation purposes.

Both editions are free for use.

mengmarmal · 02-12-2010, 08:46 AM

Thanks! I will try with it for my dataset.

wuhoucdc · 02-13-2010, 10:46 AM

Thanks a lot for the good package, Dongliang. I'll try it in my data.

Dongliang Ge · 02-20-2010, 04:54 AM

SVA now comes on a DVD.

Dongliang Ge · 03-01-2010, 08:02 AM

The website of SVA is now up:

http://www.svaproject.org/

roadrunner · 03-04-2010, 06:41 AM

Hey dongliang nice seeing you here...

Dongliang Ge · 03-08-2010, 07:09 AM

Friends,

A lite evaluation edition is released for Windows. Play with it on your laptop!

http://www.svaproject.org/download.php#win

I would also take this chance to thank all the users and their comments!

Here I have a screenshot on a Dell E6400 laptop with 32-bit Windows XP:

Larger version:

http://www.svaproject.org/images/sva_win32.png

Dongliang Ge · 06-18-2010, 07:16 AM

Whole-Genome Sequencing of a Single Proband Together with Linkage Analysis Identifies a Mendelian Disease Gene

Sobreira NLM, Cirulli ET, Avramopoulos D, Wohler E, Oswald GL, et al. (2010) PLoS Genet 6(6): e1000991. doi:10.1371/journal.pgen.1000991

http://people.genome.duke.edu/~dg48/...dromatosis.php

11-25-2009, 06:31 AM	#1
Dongliang Ge Member Join Date: Nov 2009 Location: NC, USA Posts: 18	SVA: visualizing and annotating genetic variants for next-gen seq Friends, If you are working on next-generation sequencing studies, particularly if you are interested in annotating, visualizing SNPs, INDELs, CNVs, and identifying genetic variants responsible for biological traits or diseases, please check out our software tool SequenceVariantAnalyzer (SVA): http://www.svaproject.org/ SVA is designed for two specific aims: To annotate the biological functions of the identified genetic variants, organize and visualize them; To help find the genetic variants that are associated with or responsible for the biological traits or medical outcomes of interest. The SVA release package comes with an example project extracted from 10 genomes - 5 cases and 5 controls. To reduce the size of the release package, I release only the data on chromosome X. The web page below shows that you can play with SVA and an example project to "identify (again )" the Factor VIII (F8) gene for type A hemophilia: http://www.svaproject.org/fastrun.php SVA is also featured with an integrated genome browser to help an investigator to explore the user-generated data and data from public domains. Here is a screenshot: http://www.svaproject.org/screenshot1.php Particularly, SVA genome browser allows you to conveniently 'introduce' key variants that you identified to compare and see the difference they could make. Please give it a try and let us know what you think. Lastly, I hope you may find this tool helpful for your next-generation discovery! Best regards, Dongliang Ge, Duke University, USA http://people.genome.duke.edu/~dg48/ Last edited by Dongliang Ge; 03-04-2010 at 01:26 PM.

01-23-2010, 05:07 PM	#2
Dongliang Ge Member Join Date: Nov 2009 Location: NC, USA Posts: 18	SVA is just released! Check it out at: http://www.svaproject.org/ Last edited by Dongliang Ge; 03-01-2010 at 08:00 AM.

03-08-2010, 07:09 AM	#11
Dongliang Ge Member Join Date: Nov 2009 Location: NC, USA Posts: 18	Friends, A lite evaluation edition is released for Windows. Play with it on your laptop! http://www.svaproject.org/download.php#win I would also take this chance to thank all the users and their comments! Here I have a screenshot on a Dell E6400 laptop with 32-bit Windows XP: Larger version: http://www.svaproject.org/images/sva_win32.png Last edited by Dongliang Ge; 03-08-2010 at 07:15 AM.

06-18-2010, 07:16 AM	#12
Dongliang Ge Member Join Date: Nov 2009 Location: NC, USA Posts: 18	Causal variants for metachondromatosis are identified. Whole-Genome Sequencing of a Single Proband Together with Linkage Analysis Identifies a Mendelian Disease Gene Sobreira NLM, Cirulli ET, Avramopoulos D, Wohler E, Oswald GL, et al. (2010) PLoS Genet 6(6): e1000991. doi:10.1371/journal.pgen.1000991 http://people.genome.duke.edu/~dg48/...dromatosis.php

01-23-2010, 05:08 PM	#3
Dongliang Ge Member Join Date: Nov 2009 Location: NC, USA Posts: 18	Its wiki page: http://seqanswers.com/wiki/SequenceVariantAnalyzer

02-08-2010, 05:15 AM	#4
NGSfan Member Join Date: Apr 2009 Location: Austria Posts: 90	Thanks! Looks interesting! I will have a try with it.

02-11-2010, 02:20 PM	#5
Dongliang Ge Member Join Date: Nov 2009 Location: NC, USA Posts: 18	SVA comes with two editions: 1. Standard edition : ~2.2 Gb. This edition has full annotation functions. 2. Lite Evaluation edition: ~ 250Mb. This edition does not have annotation function, but can be used to load an example project for evaluation purposes. Both editions are free for use.

02-12-2010, 08:46 AM	#6
mengmarmal Junior Member Join Date: Oct 2009 Location: NC Posts: 1	Thanks! I will try with it for my dataset.

02-13-2010, 10:46 AM	#7
wuhoucdc Member Join Date: Oct 2009 Location: Nashville Posts: 14	Thanks a lot for the good package, Dongliang. I'll try it in my data.

02-20-2010, 04:54 AM	#8
Dongliang Ge Member Join Date: Nov 2009 Location: NC, USA Posts: 18	SVA now comes on a DVD.

03-01-2010, 08:02 AM	#9
Dongliang Ge Member Join Date: Nov 2009 Location: NC, USA Posts: 18	The website of SVA is now up: http://www.svaproject.org/

03-04-2010, 06:41 AM	#10
roadrunner Junior Member Join Date: Mar 2010 Location: U.S.A Posts: 1	Hey dongliang nice seeing you here...