ABACAS Algorithmic based automatic contiguation of assembled shotgun sequences
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visualize align contiguate primer primer alignemnt visualize primer contiguate

ABACAS Description

Algorithmic based automatic contiguation of assembled shotgun sequences ABACAS intendeds to rapidly contiguate (align, order, orientate), design and visualize primers to close gaps on shotgun assembled contigs based on a reference sequence.ABACAS uses MUMmer to find the 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 Artemis 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. Requirements: · MUMmer · Artemis ACT (optional) What's New in This Release: · This is the latest release of abacas.

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