Package: abacas (1.3.1-9)

[ Source: abacas  ]

close gaps in genomic alignments from short reads

ABACAS (Algorithm Based Automatic Contiguation of Assembled Sequences) intends 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 comparison 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.

Tags: Field: Biology, Bioinformatics, Implemented in: implemented-in::perl, interface::commandline, User Interface: Text-based Interactive, Role: role::program, scope::utility

Other Packages Related to abacas

• dep: mummer

  Efficient sequence alignment of full genomes

• rec: primer3

  tool to design flanking oligo nucleotides for DNA amplification

• sug: abacas-examples

  sample data for abacas to close gaps in genomic alignments

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