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Old 03-21-2011, 08:25 AM
 
Default Bug#619100: ITP: abacas -- Algorithm Based Automatic Contiguation of Assembled Sequences

Package: wnpp
Severity: wishlist
Owner: andreas@an3as.eu

* Package name : abacas
Version : 1.3.1
Upstream Author : Wellcome Trust Sanger Institute
* URL : http://abacas.sourceforge.net/
* License : GPL
Programming Lang: Perl
Description : Algorithm Based Automatic Contiguation of Assembled Sequences
ABACAS is intended to rapidly contiguate (align, order, orientate),
visualize and design primers to close gaps on shotgun assembled contigs
based on a reference sequence.
.
ABACAS uses MUMmer to find alignment positions and identify syntenies
of assembled contigs against the reference. The output is then processed
to generate a pseudomolecule taking overlapping contigs and gaps in to
account. ABACAS generates a comparision file that can be used to
visualize ordered and oriented contigs in ACT. Synteny is represented by
red bars where colour intensity decreases with lower values of percent
identity between comparable blocks. Information on contigs such as the
orientation, percent identity, coverage and overlap with other contigs
can also be visualized by loading the outputted feature file on ACT.

The packaging will be done in the Debian Med team and is available in SVN at

Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/abacas/trunk/


-- System Information:
Debian Release: squeeze/sid
APT prefers oldstable
APT policy: (500, 'oldstable'), (50, 'unstable')
Architecture: i386 (i686)



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