title: ABACAS: algorithm-based automatic contiguation of assembled sequences.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  ABACAS is implemented in Perl and is freely available for download from http://abacas.sourceforge.net.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK. sa4@sanger.ac.uk
authors.forename: Samuel
authors.initials: S
authors.lastname: Assefa
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Keane
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Otto
authors.forename: Chris
authors.initials: C
authors.lastname: Newbold
authors.forename: Matthew
authors.initials: M
authors.lastname: Berriman
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software