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abacas

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.

Homepage:
Package version:1.3.1-1
Architecture:all
Distribution:Debian
Filename:abacas_1.3.1-1_all.deb

/usr/share/man/man1/abacas.1.gz

ABACAS(1)                   User Commands                  ABACAS(1)



NAME
       abacas  - Algorithm Based Automatic Contiguation of Assembled
       Sequences

SYNOPSIS
       abacas -r ref -q qs -p prog  [OPTIONS]

       OR

       abacas -r ref -q psf -e

       ref    reference sequence in a single fasta file

       qs     contigs in multi-fasta format

       rog    MUMmer program to use
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/usr/share/doc/abacas/changelog.Debian.gz

abacas (1.3.1-1) unstable; urgency=low

  * Initial release (Closes: #619100)

 -- Andreas Tille <tille@debian.org>  Mon, 21 Mar 2011 09:48:04 +0100

/usr/share/doc/abacas/copyright

Format: http://dep.debian.net/deps/dep5/
Upstream-Name: Abacas
Upstream-Contact: Wellcome Trust Sanger Institute <sa4@sanger.ac.uk>
Source:  http://sourceforge.net/projects/abacas/files/

Copyright: © 2008-10 Genome Research Limited. All Rights Reserved.
License: GPL-2+
	
	Abacas is free software; you can redistribute it and/or modify
	it under the terms of the GNU General Public License as publi
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