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A vertebrate case study of the quality of assemblies derived from next-generation sequences

Liang Ye1, LaDeana W Hillier1, Patrick Minx1, Nay Thane1, Devin P Locke1, John C Martin1, Lei Chen1, Makedonka Mitreva1, Jason R Miller2, Kevin V Haub1, David J Dooling1, Elaine R Mardis1, Richard K Wilson1, George M Weinstock1 and Wesley C Warren1*

Author Affiliations

1 The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA

2 The J Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850, USA

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Genome Biology 2011, 12:R31 doi:10.1186/gb-2011-12-3-r31

Published: 31 March 2011

Abstract

The unparalleled efficiency of next-generation sequencing (NGS) has prompted widespread adoption, but significant problems remain in the use of NGS data for whole genome assembly. We explore the advantages and disadvantages of chicken genome assemblies generated using a variety of sequencing and assembly methodologies. NGS assemblies are equivalent in some ways to a Sanger-based assembly yet deficient in others. Nonetheless, these assemblies are sufficient for the identification of the majority of genes and can reveal novel sequences when compared to existing assembly references.