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- Title
ABACAS: algorithm-based automatic contiguation of assembled sequences.
- Authors
Samuel Assefa; Thomas M. Keane; Thomas D. Otto; Chris Newbold; Matthew Berriman
- 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@sanger.ac.uk
- Publication
Bioinformatics, 2009, Vol 25, Issue 15, p1968
- ISSN
1367-4803
- Publication type
Academic Journal
- DOI
10.1093/bioinformatics/btp347