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Genome Biol. 2010;11(4):R41. doi: 10.1186/gb-2010-11-4-r41. Epub 2010 Apr 13.

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

Author information

  • 1Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. jit@sanger.ac.uk

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.

PMID:
20388197
[PubMed - indexed for MEDLINE]
PMCID:
PMC2884544
Free PMC Article

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