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https://forum.ugene.net/forum/YaBB.pl General Category >> Feature Requests >> Contig Assembly on trace files https://forum.ugene.net/forum/YaBB.pl?num=1297229839 Message started by Fel on Feb 9^th, 2011 at 12:37pm

Title: Contig Assembly on trace files
Post by Fel on Feb 9^th, 2011 at 12:37pm

Hi, I'm new to ugene, but I got a very good impression on it! I read some topics about DNA assembly, but I'm not sure if you intent to introduce a contig assembly tool that allow us to work directly on chromatogram files, while inspecting trace quality.

Thanks

Fel
Brazil

Title: Re: Contig Assembly on trace files
Post by Peacemaker on Feb 9^th, 2011 at 2:01pm

This would be a very useful tool ineed. Especially the contig assembly of several overlapping sequencing (.ab1) files without the need of a reference sequence is often used in molecular biology. Until now, the assembly tool already implemented into Ugene requires a reference sequence as far as I have understood. I' m thinking of a function like "Contig Express" in Vector NTI (Invitrogen). It would be very useful to include something like this into Ugene.
Best Regards

Title: Re: Contig Assembly on trace files
Post by clemensvb on Feb 9^th, 2011 at 5:25pm

Hi there!

I would like to join the oppinion of the thread starter. Ugene is really a great tool. For my lab workflow a contig assembly tool would be very helpful. So if you could integrate this feature in ugene this would be great!

Thanks.

Title: Re: Contig Assembly on trace files
Post by Konstantin Okonechnikov on Feb 9^th, 2011 at 6:12pm

Looks like contig assembly is really demanded.

Maybe someone knows, if there is a good open-source tool we can integrate into UGENE?
So far I've heard about AMOS (too "big" for UGENE yet) and CAP.

P.S. Thanks for all kind words and feedback :)

Title: Re: Contig Assembly on trace files
Post by Agu on Feb 9^th, 2011 at 8:02pm

I don't know about any open source project, but what about CAP3 as a plug-in? That might be a fast way to have this feature in UGENE.

You can find different flavours here:
http://seq.cs.iastate.edu/cap3.html

And a very good description of the program (including input and output files) here:
http://deepc2.psi.iastate.edu/aat/cap/capdoc.html

Edit:
Checking the last link, I found this open source project:
http://staden.sourceforge.net/

Title: Re: Contig Assembly on trace files
Post by ra on Mar 27^th, 2011 at 10:25pm

I agree that this is a very basic and important feature.

cap3 and Mira3 could be good choices for assemblers.

Title: Re: Contig Assembly on trace files
Post by Mikhail Fursov on Mar 29^th, 2011 at 10:44am

ra wrote on Mar 27^th, 2011 at 10:25pm:

I agree that this is a very basic and important feature.

cap3 and Mira3 could be good choices for assemblers.

We plan adding assembly viewer with the next release (v1.9.3). This will untie our hands on related features implementation. So with the release after 1.9.3 we will consider integration of one of these packages.

Title: Re: Contig Assembly on trace files
Post by vixen sjlin on Aug 14^th, 2013 at 11:16pm

Staden Package is a very nice program for contig assembly, however, the source of the core program "Phred/Phrap/Consed" is still required to be requested from U of W.

https://sourceforge.net/project/screenshots.php?group_id=100316

I requested to have a translation function of assembled contigs, would you please also consider that? Thanks!
http://ugene.unipro.ru/forum/YaBB.pl?num=1368220000

Title: Re: Contig Assembly on trace files
Post by BMBinfo on Mar 25^th, 2014 at 12:28am

I was wondering if any progress has been made with this feature. I am using 1.13.1.

Thanks

Title: Re: Contig Assembly on trace files
Post by Konstantin Okonechnikov on Mar 27^th, 2014 at 12:04am

Hi! The CAP3 tool is integrated into UGENE for contig assembly. See more documentation here:
http://ugene.unipro.ru/documentation/manual/plugins/cap3.html