This software automates the organization of assembled shotgun sequences using algorithms.
If you're looking for a quick and efficient way to align, order, orientate, design and visualize primers to close gaps on shotgun assembled contigs, then ABACAS is the software for you. Using MUMmer, ABACAS finds the alignment positions and identifies syntenies of assembled contigs against the reference, and generates a pseudomolecule that takes overlaps and gaps into account.
The output from ABACAS is in the form of a comparison file that can be used to visualize the ordered and oriented contigs in Artemis ACT. The synteny is represented by red bars, with the color intensity decreasing as the percent identity between comparable blocks decreases.
In addition to the visual representation of the contigs, ABACAS also provides information on contigs such as the orientation, percent identity, coverage, and overlap with other contigs. This information can be visualized by loading the outputted feature file on ACT.
Overall, ABACAS is an excellent tool for anyone working with shotgun assembled contigs who needs to close gaps and visualize contigs in a rapid and efficient manner.
The output from ABACAS is in the form of a comparison file that can be used to visualize the ordered and oriented contigs in Artemis ACT. The synteny is represented by red bars, with the color intensity decreasing as the percent identity between comparable blocks decreases.
In addition to the visual representation of the contigs, ABACAS also provides information on contigs such as the orientation, percent identity, coverage, and overlap with other contigs. This information can be visualized by loading the outputted feature file on ACT.
Overall, ABACAS is an excellent tool for anyone working with shotgun assembled contigs who needs to close gaps and visualize contigs in a rapid and efficient manner.
What's New
Version 1.1: N/A