SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations
SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS...
| Main Authors: | , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Oxford University Press
2015
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/67422 |
| _version_ | 1855515562571988992 |
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| author | Dereeper, Alexis Homa, Felix Andres, Gwendoline Sempéré, Guilhem Sarah, Gautier Hueber, Yann Dufayard, Jean-François Ruíz, Manuel |
| author_browse | Andres, Gwendoline Dereeper, Alexis Dufayard, Jean-François Homa, Felix Hueber, Yann Ruíz, Manuel Sarah, Gautier Sempéré, Guilhem |
| author_facet | Dereeper, Alexis Homa, Felix Andres, Gwendoline Sempéré, Guilhem Sarah, Gautier Hueber, Yann Dufayard, Jean-François Ruíz, Manuel |
| author_sort | Dereeper, Alexis |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr. |
| format | Journal Article |
| id | CGSpace67422 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2015 |
| publishDateRange | 2015 |
| publishDateSort | 2015 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace674222025-03-13T09:43:59Z SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations Dereeper, Alexis Homa, Felix Andres, Gwendoline Sempéré, Guilhem Sarah, Gautier Hueber, Yann Dufayard, Jean-François Ruíz, Manuel genetic variation data analysis computer applications databases genetic polymorphism genotypes genomes variación genetica análisis de datos aplicaciones del ordenador bases de datos polimorfismo genético genotipos genomas genetics SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr. 2015-07-01 2015-07-27T21:19:04Z 2015-07-27T21:19:04Z Journal Article https://hdl.handle.net/10568/67422 en Open Access Oxford University Press Dereeper, Alexis; Homa, Felix; Andres, Gwendoline; Sempere, Guilhem; Sarah, Gautier; Hueber, Yann; Dufayard, Jean-François; Ruiz, Manuel. 2015. SNiPlay3 : a web-based application for exploration and large scale analyses of genomic variations. Nucleic Acids Research 43(W1): W295-W300. |
| spellingShingle | genetic variation data analysis computer applications databases genetic polymorphism genotypes genomes variación genetica análisis de datos aplicaciones del ordenador bases de datos polimorfismo genético genotipos genomas genetics Dereeper, Alexis Homa, Felix Andres, Gwendoline Sempéré, Guilhem Sarah, Gautier Hueber, Yann Dufayard, Jean-François Ruíz, Manuel SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations |
| title | SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations |
| title_full | SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations |
| title_fullStr | SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations |
| title_full_unstemmed | SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations |
| title_short | SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations |
| title_sort | sniplay3 a web based application for exploration and large scale analyses of genomic variations |
| topic | genetic variation data analysis computer applications databases genetic polymorphism genotypes genomes variación genetica análisis de datos aplicaciones del ordenador bases de datos polimorfismo genético genotipos genomas genetics |
| url | https://hdl.handle.net/10568/67422 |
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