Difference between revisions of "Abacas"
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|Version download=http://ftp.debian.org/debian/pool/main/a/abacas/abacas_1.3.1.orig.tar.gz | |Version download=http://ftp.debian.org/debian/pool/main/a/abacas/abacas_1.3.1.orig.tar.gz | ||
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Revision as of 04:11, 14 February 2018
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
License
Verified by
Verified on
Notes
License
Verified by
Debian: Andreas Tille <tille@debian.org>
Verified on
25 October 2013
Notes
License: gpl-2+
Leaders and contributors
| Contact(s) | Role |
|---|---|
| Wellcome Trust Sanger Institute | contact |
Resources and communication
| Audience | Resource type | URI |
|---|---|---|
| Debian (Ref) | https://tracker.debian.org/pkg/abacas | |
| Download | http://sourceforge.net/projects/abacas/files/ |
Software prerequisites
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.