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ABACAS 1.3.1

 
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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.

Platforms: Mac , Mac OS X

System requirements: MUMmer

 
Added: 17 September, 2012 File size: 61.4 KB
Status: new Download times: 512 kb/s: < 1 sec
Program type: freeware   1 Mb/s: < 1 sec
      2 Mb/s: < 1 sec
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Tags: Contigs, Assembled, Visualize, Abacas, Percent, Reference, Identity, Lower, Values, Decreases, Colour, Oriented, Ordered, Synteny, Represented, Intensity, Comparable, Visualized

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