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 |
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Status: | Published |
Refereed: | Yes |
Glasgow Author(s) Enlighten ID: | Otto, Professor Thomas |
Authors: | Assefa, S., Keane, T. M., Otto, T. D., Newbold, C., and Berriman, M. |
College/School: | College of Medical Veterinary and Life Sciences > School of Infection & Immunity |
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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