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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.


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

Leaders and contributors

Wellcome Trust Sanger Institute contact

Resources and communication

AudienceResource typeURI
Debian (Ref)https://tracker.debian.org/pkg/abacas

Software prerequisites

This entry (in part or in whole) was last reviewed on 1 February 2018.


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


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