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SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations.
Dereeper, Alexis; Homa, Felix; Andres, Gwendoline; Sempere, Guilhem; Sarah, Gautier; Hueber, Yann; Dufayard, Jean-François; Ruiz, Manuel.
Afiliación
  • Dereeper A; UMR Interaction Plante-Microorganismes et Environnement (IPME), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France alexis.dereeper@ird.fr.
  • Homa F; UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France.
  • Andres G; UPMC, CNRS, ABiMS Station Biologique, 29680 Roscoff, France.
  • Sempere G; UMR Intertryp CIRAD, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France.
  • Sarah G; UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France.
  • Hueber Y; Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.
  • Dufayard JF; UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France.
  • Ruiz M; UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France Agrobiodiversity research area, International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia.
Nucleic Acids Res ; 43(W1): W295-300, 2015 Jul 01.
Article en En | MEDLINE | ID: mdl-26040700
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Variación Genética / Programas Informáticos / Polimorfismo de Nucleótido Simple / Genómica Idioma: En Revista: Nucleic Acids Res Año: 2015 Tipo del documento: Article País de afiliación: Francia Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Variación Genética / Programas Informáticos / Polimorfismo de Nucleótido Simple / Genómica Idioma: En Revista: Nucleic Acids Res Año: 2015 Tipo del documento: Article País de afiliación: Francia Pais de publicación: Reino Unido