ABACAS: algorithm-based automatic contiguation of assembled sequences

Assefa, S., Keane, T. M., Otto, T. D. , Newbold, C. and Berriman, M. (2009) ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics, 25(15), pp. 1968-1969. (doi:10.1093/bioinformatics/btp347) (PMID:19497936) (PMCID:PMC2712343)

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Abstract

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.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Otto, Dr Thomas
Authors: Assefa, S., Keane, T. M., Otto, T. D., Newbold, C., and Berriman, M.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Bioinformatics
Publisher:Oxford University Press
ISSN:1367-4803
ISSN (Online):1460-2059
Copyright Holders:Copyright ©2009 The Authors
First Published:First published in Bioinformatics 25 (15):1968-1969
Publisher Policy:Reproduced under a Creative Commons License

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