SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Browsers/Viewers for RNAseq Xi Wang Bioinformatics 43 08-08-2010 11:33 PM
[request] ngs comparison seqmaster Bioinformatics 0 07-30-2010 02:27 AM
spliced alignments viewers? darked89 Bioinformatics 4 04-28-2010 04:36 AM
Comparison of NGS analyser tech info gavin.oliver General 21 04-06-2010 12:30 AM
most commonly used alignment viewers nat Bioinformatics 1 08-12-2009 01:02 AM

Reply
 
Thread Tools
Old 04-07-2011, 07:28 AM   #1
Martino
Member
 
Location: Netherlands

Join Date: Apr 2011
Posts: 15
Default Items for comparison between NGS viewers.

Dear,

At the moment, I am making a report about the comparison of different NGS Viewers.

My question is:

Do you know items or subjects at which I can compare all those NGS viewers with each other for my report?

Thank you for your help!
Martino is offline   Reply With Quote
Old 04-07-2011, 09:26 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542
Default

Homework?

There is an out of date comparison here - note that all these tools have been updated since:
http://jermdemo.blogspot.com/2010/08...-reviewed.html
maubp is offline   Reply With Quote
Old 04-07-2011, 01:23 PM   #3
tnabtaf
Member
 
Location: Oregon

Join Date: Jan 2011
Posts: 53
Default

There was a great paper in a Nature Methods supplement last year on genome browsing and browsers: Visualizing genomes: techniques and challenges by Nielsen et al. This is part of a whole supplement on Visualizing Biological Data.
tnabtaf is offline   Reply With Quote
Old 04-08-2011, 12:07 AM   #4
Martino
Member
 
Location: Netherlands

Join Date: Apr 2011
Posts: 15
Default Thanks!

Dear,

Thanks for your help!

I also have names of other NGS viewers.

Shall I mention them here?
Martino is offline   Reply With Quote
Old 04-08-2011, 12:55 AM   #5
Thorondor
Member
 
Location: Heidelberg

Join Date: Feb 2011
Posts: 69
Default

sure, any information is appreciated. Especially the pros and cons for these viewers and your favorite one.
Thorondor is offline   Reply With Quote
Old 04-08-2011, 01:55 AM   #6
Martino
Member
 
Location: Netherlands

Join Date: Apr 2011
Posts: 15
Default

The 10 NGS Viewers I found are:

1. CLCBio
2. Integrative Genomics Viewer (IGV)
3. Magic Viewer
4. Galaxy
5. Genomatrix
6. JMP Genomics
7. NextGENe
8. SeqMan Genome Analyser
9. SHORE
10. Top Hat

I hope I can help you with this information.
Martino is offline   Reply With Quote
Old 04-08-2011, 02:03 AM   #7
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542
Default

And missing from your list but on the link I gave,

11. tview
12. BamView (and Artemis with the BamView plugin)
13. GenoViewer
14. Tablet
maubp is offline   Reply With Quote
Old 04-08-2011, 02:13 AM   #8
AdamB
Member
 
Location: uk

Join Date: Apr 2010
Posts: 43
Default

15. SeqMonk
16. Partek

There are loads out there!
AdamB is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:41 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO