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SUMMARY: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated. AVAILABILITY AND IMPLEMENTATION: ABACAS is implemented in Perl and is freely available for download from http://abacas.sourceforge.net.

Original publication

DOI

10.1093/bioinformatics/btp347

Type

Journal article

Journal

Bioinformatics

Publication Date

01/08/2009

Volume

25

Pages

1968 - 1969

Keywords

Algorithms, Computational Biology, Sequence Alignment, Sequence Analysis, DNA, Software