Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

Tsai, I. J., Otto, T. D. and Berriman, M. (2010) Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biology, 11, R41. (doi: 10.1186/gb-2010-11-4-r41) (PMID:20388197) (PMCID:PMC2884544)

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Abstract

Advances in sequencing technology allow genomes to be sequenced at vastly decreased costs. However, the assembled data frequently are highly fragmented with many gaps. We present a practical approach that uses Illumina sequences to improve draft genome assemblies by aligning sequences against contig ends and performing local assemblies to produce gap-spanning contigs. The continuity of a draft genome can thus be substantially improved, often without the need to generate new data.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Otto, Dr Thomas
Authors: Tsai, I. J., Otto, T. D., and Berriman, M.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Genome Biology
Publisher:BioMed Central
ISSN:1465-6906
ISSN (Online):1465-6906
Copyright Holders:Copyright ©2010 Tsai et al.
First Published:First published in Genome Biology 11:R41
Publisher Policy:Reproduced under a Creative Commons License

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