Journal
BIOINFORMATICS
Volume 25, Issue 15, Pages 1968-1969Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btp347
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Funding
- Wellcome Trust [WT085775/Z/08/Z]
- European Union 6th Framework Program [LSHP-LT-2004-503578]
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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.
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