Journal Article

ABACAS: algorithm-based automatic contiguation of assembled sequences

Samuel Assefa, Thomas M. Keane, Thomas D. Otto, Chris Newbold and Matthew Berriman

in Bioinformatics

Volume 25, issue 15, pages 1968-1969
Published in print August 2009 | ISSN: 1367-4803
Published online June 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp347

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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

Contact: sa4@sanger.ac.uk

Journal Article.  1201 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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