Cargando…
A vertebrate case study of the quality of assemblies derived from next-generation sequences
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 ass...
| Autores principales: | , , , , , , , , , , , , , , |
|---|---|
| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
BioMed Central
2011
|
| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129681/ https://www.ncbi.nlm.nih.gov/pubmed/21453517 http://dx.doi.org/10.1186/gb-2011-12-3-r31 |
| _version_ | 1782207554704637952 |
|---|---|
| author | Ye, Liang Hillier, LaDeana W Minx, Patrick Thane, Nay Locke, Devin P Martin, John C Chen, Lei Mitreva, Makedonka Miller, Jason R Haub, Kevin V Dooling, David J Mardis, Elaine R Wilson, Richard K Weinstock, George M Warren, Wesley C |
| author_facet | Ye, Liang Hillier, LaDeana W Minx, Patrick Thane, Nay Locke, Devin P Martin, John C Chen, Lei Mitreva, Makedonka Miller, Jason R Haub, Kevin V Dooling, David J Mardis, Elaine R Wilson, Richard K Weinstock, George M Warren, Wesley C |
| author_sort | Ye, Liang |
| collection | PubMed |
| description | 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. |
| format | Online Article Text |
| id | pubmed-3129681 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2011 |
| publisher | BioMed Central |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-31296812011-07-06 A vertebrate case study of the quality of assemblies derived from next-generation sequences Ye, Liang Hillier, LaDeana W Minx, Patrick Thane, Nay Locke, Devin P Martin, John C Chen, Lei Mitreva, Makedonka Miller, Jason R Haub, Kevin V Dooling, David J Mardis, Elaine R Wilson, Richard K Weinstock, George M Warren, Wesley C Genome Biol Method 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. BioMed Central 2011 2011-03-31 /pmc/articles/PMC3129681/ /pubmed/21453517 http://dx.doi.org/10.1186/gb-2011-12-3-r31 Text en Copyright ©2011 Ye et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| spellingShingle | Method Ye, Liang Hillier, LaDeana W Minx, Patrick Thane, Nay Locke, Devin P Martin, John C Chen, Lei Mitreva, Makedonka Miller, Jason R Haub, Kevin V Dooling, David J Mardis, Elaine R Wilson, Richard K Weinstock, George M Warren, Wesley C A vertebrate case study of the quality of assemblies derived from next-generation sequences |
| title | A vertebrate case study of the quality of assemblies derived from next-generation sequences |
| title_full | A vertebrate case study of the quality of assemblies derived from next-generation sequences |
| title_fullStr | A vertebrate case study of the quality of assemblies derived from next-generation sequences |
| title_full_unstemmed | A vertebrate case study of the quality of assemblies derived from next-generation sequences |
| title_short | A vertebrate case study of the quality of assemblies derived from next-generation sequences |
| title_sort | vertebrate case study of the quality of assemblies derived from next-generation sequences |
| topic | Method |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129681/ https://www.ncbi.nlm.nih.gov/pubmed/21453517 http://dx.doi.org/10.1186/gb-2011-12-3-r31 |
| work_keys_str_mv | AT yeliang avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT hillierladeanaw avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT minxpatrick avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT thanenay avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT lockedevinp avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT martinjohnc avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT chenlei avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT mitrevamakedonka avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT millerjasonr avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT haubkevinv avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT doolingdavidj avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT mardiselainer avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT wilsonrichardk avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT weinstockgeorgem avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT warrenwesleyc avertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT yeliang vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT hillierladeanaw vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT minxpatrick vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT thanenay vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT lockedevinp vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT martinjohnc vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT chenlei vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT mitrevamakedonka vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT millerjasonr vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT haubkevinv vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT doolingdavidj vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT mardiselainer vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT wilsonrichardk vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT weinstockgeorgem vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences AT warrenwesleyc vertebratecasestudyofthequalityofassembliesderivedfromnextgenerationsequences |