Bug#619100: ITP: abacas -- Algorithm Based Automatic Contiguation of Assembled Sequences

[andreas@an3as.eu]

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)