ABACAS: Algorithm-Based Automatic Contiguation of Assembled Sequences

Bioinformatics. 2009 Aug 1;25(15):1968-9. doi: 10.1093/bioinformatics/btp347. Epub 2009 Jun 3.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Computational Biology / methods*
  • Sequence Alignment
  • Sequence Analysis, DNA / methods*
  • Software*