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

Isheng J Tsai*, Thomas D Otto and Matthew Berriman

Author Affiliations

Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

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Genome Biology 2010, 11:R41  doi:10.1186/gb-2010-11-4-r41

Published: 13 April 2010

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.