ABACAS: algorithm-based automatic contiguation of assembled sequences.

Journal article

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.

Authors: Assefa, S; Keane, T; Otto, T; Newbold, C; Berriman, M

• Publication status: Published
• Journal: Bioinformatics (Oxford, England)
• Volume: 25
• Issue: 15
• Pages: 1968-1969
• Publication date: 2009-08-01
• DOI: 10.1093/bioinformatics/btp347
• EISSN: 1367-4811
• ISSN: 1367-4803
• Language: English
• Keywords: Software; Computational Biology; Sequence Alignment; Algorithms; Sequence Analysis, DNA