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Bioinformatics Advance Access originally published online on June 3, 2009
Bioinformatics 2009 25(15):1968-1969; doi:10.1093/bioinformatics/btp347
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

ABACAS: algorithm-based automatic contiguation of assembled sequences

Samuel Assefa 1,*, Thomas M. Keane 1, Thomas D. Otto 1, Chris Newbold 1,2 and Matthew Berriman 1

1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA and 2 Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK

* To whom correspondence should be addressed.


  Abstract

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{at}sanger.ac.uk

Associate Editor: Alfonso Valencia

Received on April 27, 2009; revised on May 28, 2009; accepted on May 28, 2009

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