An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments
Recent advances in high-throughput sequencing (HTS) technologies and computing capacity have produced unprecedented amounts of genomic data that have unraveled the genetics of phenotypic variability in several species. However, operating and integrating current software tools for data analysis still...
| Main Authors: | , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Oxford University Press
2014
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/41897 |
| _version_ | 1855525090518630400 |
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| author | Duitama, Jorge Quintero, Juan Camilo Cruz, Daniel Felipe Quintero, Constanza Hubmann, Georg Foulquié Moreno, Maria R. Verstrepen, Kevin J. Trevelein, Johan M Tohme, Joseph M. |
| author_browse | Cruz, Daniel Felipe Duitama, Jorge Foulquié Moreno, Maria R. Hubmann, Georg Quintero, Constanza Quintero, Juan Camilo Tohme, Joseph M. Trevelein, Johan M Verstrepen, Kevin J. |
| author_facet | Duitama, Jorge Quintero, Juan Camilo Cruz, Daniel Felipe Quintero, Constanza Hubmann, Georg Foulquié Moreno, Maria R. Verstrepen, Kevin J. Trevelein, Johan M Tohme, Joseph M. |
| author_sort | Duitama, Jorge |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Recent advances in high-throughput sequencing (HTS) technologies and computing capacity have produced unprecedented amounts of genomic data that have unraveled the genetics of phenotypic variability in several species. However, operating and integrating current software tools for data analysis still require important investments in highly skilled personnel. Developing accurate, efficient and user-friendly software packages for HTS data analysis will lead to a more rapid discovery of genomic elements relevant to medical, agricultural and industrial applications. We therefore developed Next-Generation Sequencing Eclipse Plug-in (NGSEP), a new software tool for integrated, efficient and user-friendly detection of single nucleotide variants (SNVs), indels and copy number variants (CNVs). NGSEP includes modules for read alignment, sorting, merging, functional annotation of variants, filtering and quality statistics. Analysis of sequencing experiments in yeast, rice and human samples shows that NGSEP has superior accuracy and efficiency, compared with currently available packages for variants detection. We also show that only a comprehensive and accurate identification of repeat regions and CNVs allows researchers to properly separate SNVs from differences between copies of repeat elements. We expect that NGSEP will become a strong support tool to empower the analysis of sequencing data in a wide range of research projects on different species. |
| format | Journal Article |
| id | CGSpace41897 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2014 |
| publishDateRange | 2014 |
| publishDateSort | 2014 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace418972025-03-13T09:44:15Z An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments Duitama, Jorge Quintero, Juan Camilo Cruz, Daniel Felipe Quintero, Constanza Hubmann, Georg Foulquié Moreno, Maria R. Verstrepen, Kevin J. Trevelein, Johan M Tohme, Joseph M. rice arroz genotypes genotipos Recent advances in high-throughput sequencing (HTS) technologies and computing capacity have produced unprecedented amounts of genomic data that have unraveled the genetics of phenotypic variability in several species. However, operating and integrating current software tools for data analysis still require important investments in highly skilled personnel. Developing accurate, efficient and user-friendly software packages for HTS data analysis will lead to a more rapid discovery of genomic elements relevant to medical, agricultural and industrial applications. We therefore developed Next-Generation Sequencing Eclipse Plug-in (NGSEP), a new software tool for integrated, efficient and user-friendly detection of single nucleotide variants (SNVs), indels and copy number variants (CNVs). NGSEP includes modules for read alignment, sorting, merging, functional annotation of variants, filtering and quality statistics. Analysis of sequencing experiments in yeast, rice and human samples shows that NGSEP has superior accuracy and efficiency, compared with currently available packages for variants detection. We also show that only a comprehensive and accurate identification of repeat regions and CNVs allows researchers to properly separate SNVs from differences between copies of repeat elements. We expect that NGSEP will become a strong support tool to empower the analysis of sequencing data in a wide range of research projects on different species. 2014-04-01 2014-08-06T06:55:02Z 2014-08-06T06:55:02Z Journal Article https://hdl.handle.net/10568/41897 en Open Access Oxford University Press Duitama J, Quintero JC, Cruz DF, Quintero C, Hubmann G, Foulquié-Moreno MR, Verstrepen KJ, Thevelein JM, and Tohme J. 2014. An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments. Nucleic Acids Research. 42 (6): e44 |
| spellingShingle | rice arroz genotypes genotipos Duitama, Jorge Quintero, Juan Camilo Cruz, Daniel Felipe Quintero, Constanza Hubmann, Georg Foulquié Moreno, Maria R. Verstrepen, Kevin J. Trevelein, Johan M Tohme, Joseph M. An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments |
| title | An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments |
| title_full | An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments |
| title_fullStr | An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments |
| title_full_unstemmed | An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments |
| title_short | An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments |
| title_sort | integrated framework for discovery and genotyping of genomic variants from high throughput sequencing experiments |
| topic | rice arroz genotypes genotipos |
| url | https://hdl.handle.net/10568/41897 |
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