Abacas

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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

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

AudienceResource typeURI
Downloadhttp://sourceforge.net/projects/abacas/files/
Debian (Ref)https://tracker.debian.org/pkg/abacas


Software prerequisites

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



Entry




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

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