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Genome Res. 2010 Sep;20(9):1165-73. doi: 10.1101/gr.101360.109. Epub 2010 May 27.

Assembly of large genomes using second-generation sequencing.

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  • 1Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA.

Abstract

Second-generation sequencing technology can now be used to sequence an entire human genome in a matter of days and at low cost. Sequence read lengths, initially very short, have rapidly increased since the technology first appeared, and we now are seeing a growing number of efforts to sequence large genomes de novo from these short reads. In this Perspective, we describe the issues associated with short-read assembly, the different types of data produced by second-gen sequencers, and the latest assembly algorithms designed for these data. We also review the genomes that have been assembled recently from short reads and make recommendations for sequencing strategies that will yield a high-quality assembly.

PMID:
20508146
PMCID:
PMC2928494
DOI:
10.1101/gr.101360.109
[PubMed - indexed for MEDLINE]
Free PMC Article
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