visualization tools for sequence alignments and assembling

[dicty]

Hi,

Can anyone suggest any good visualization tools for sequence alignments and assembling?

Thanks,

Dicty

[steven]

The seqanswers wiki is your friend. Examples with:
- assembly visualization
- visualization
- genome browser
There is also a huge thread somewhere about genome browsers, with tablet, igv, igb, jbrowse, etc etc.. i would use the search function of the forum (up there).

[dicty]

Thanks a lot for your response. It's very helpful.

[jkbonfield]

If you have a genuine assembly that you wish to *edit*, the choice is more restricted. I'll declare an interest/bias as I'm the primary author of Gap5, however I believe Consed has also received updates to allow it to edit NGS assemblies.

That said, if it's just visualisation that you need then the myriad of tools out there listed in the links above will do a fine job, and indeed many will be better than Gap5 would due to DAS source integration and proper handling of reference based coordinates.

https://sourceforge.net/projects/staden/

[dicty]

Thanks a lot, jkbonfield. Currently I only want to visualize the alignment and assembly results, but probably I will use Staden for further analysis.