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.
Fig1. ABACAS workflow
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.Screen shots
Fig2. Artemis view of 3D7 FuzzyPaths Solexa contigs ordered against 3D7
Fig3. Chromosome 14 of morphed Pf IT with capillary contigs compared to Pf 3D7
Additional information
A poster presented at BioMalPar 2009 conference could be found here.
