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

Liang Ye; La Deana W. Hillier; Patrick Minx; Nay Thane; Devin P. Locke; John C. Martin; Lei Chen; Makedonka Mitreva; Jason R. Miller; Kevin V. Haub; David J. Dooling; Elaine R. Mardis; Richard K. Wilson; George M. Weinstock; Wesley C. Warren

doi:10.1186/gb-2011-12-3-r31

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

Liang Ye, La Deana W. Hillier, Patrick Minx, Nay Thane, Devin P. Locke, John C. Martin, Lei Chen, Makedonka Mitreva, Jason R. Miller, Kevin V. Haub, David J. Dooling, Elaine R. Mardis, Richard K. Wilson, George M. Weinstock, Wesley C. Warren

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26 Scopus citations

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.

Original language	English
Article number	R31
Journal	Genome biology
Volume	12
Issue number	3
DOIs	https://doi.org/10.1186/gb-2011-12-3-r31
State	Published - Mar 31 2011

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Ye, L., Hillier, L. D. W., Minx, P., Thane, N., Locke, D. P., Martin, J. C., Chen, L., Mitreva, M., Miller, J. R., Haub, K. V., Dooling, D. J., Mardis, E. R., Wilson, R. K., Weinstock, G. M., & Warren, W. C. (2011). A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome biology, 12(3), [R31]. https://doi.org/10.1186/gb-2011-12-3-r31

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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.",

author = "Liang Ye and Hillier, {La Deana W.} and Patrick Minx and Nay Thane and Locke, {Devin P.} and Martin, {John C.} and Lei Chen and Makedonka Mitreva and Miller, {Jason R.} and Haub, {Kevin V.} and Dooling, {David J.} and Mardis, {Elaine R.} and Wilson, {Richard K.} and Weinstock, {George M.} and Warren, {Wesley C.}",

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AU - Locke, Devin P.

AU - Martin, John C.

AU - Chen, Lei

AU - Mitreva, Makedonka

AU - Miller, Jason R.

AU - Haub, Kevin V.

AU - Dooling, David J.

AU - Mardis, Elaine R.

AU - Wilson, Richard K.

AU - Weinstock, George M.

AU - Warren, Wesley C.

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AB - 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.

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

Abstract

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