Bioinformatics. 2009 Aug 1;25(15):1968-9. Epub 2009 Jun 3.

ABACAS: algorithm-based automatic contiguation of assembled sequences.

Assefa S, Keane TM, Otto TD, Newbold C, Berriman M.

Source

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK. sa4@sanger.ac.uk

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.

PMID:: 19497936; [PubMed - indexed for MEDLINE]
PMCID:: PMC2712343

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WT085775/Z/08/Z/Wellcome Trust/United Kingdom

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