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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.
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 more»
abacas (1.3.1-1) unstable; urgency=low * Initial release (Closes: #619100) -- Andreas Tille <email@example.com> Mon, 21 Mar 2011 09:48:04 +0100
Format: http://dep.debian.net/deps/dep5/ Upstream-Name: Abacas Upstream-Contact: Wellcome Trust Sanger Institute <firstname.lastname@example.org> 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 more»