Abacas

From Free Software Directory
 
Jump to: navigation, search
[edit]

Abacas

http://abacas.sourceforge.net/
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.




Licensing

LicenseVerified byVerified onNotes
License:GPLv2orlaterDebian: Andreas Tille <tille@debian.org>25 October 2013
License: gpl-2+



Leaders and contributors

Contact(s)Role
Wellcome Trust Sanger Institute contact


Resources and communication

AudienceResource typeURI
Downloadhttp://sourceforge.net/projects/abacas/files/


Software prerequisites



Entry



Date 2015-07-17
Source Debian
Source link http://packages.debian.org/sid/abacas

[[Category:]]





"contact" is not in the list (Maintainer, Contributor, Developer, Sponsor, Unknown) of allowed values for the "Role" property.






Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the page “GNU Free Documentation License”.

The copyright and license notices on this page only apply to the text on this page. Any software or copyright-licenses or other similar notices described in this text has its own copyright notice and license, which can usually be found in the distribution or license text itself.