title: SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations.
abstract: 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.
authors.affiliation: 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.
authors.forename: Alexis
authors.initials: A
authors.lastname: Dereeper
authors.affiliation: UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France.
authors.forename: Felix
authors.initials: F
authors.lastname: Homa
authors.affiliation: UPMC, CNRS, ABiMS Station Biologique, 29680 Roscoff, France.
authors.forename: Gwendoline
authors.initials: G
authors.lastname: Andres
authors.affiliation: UMR Intertryp CIRAD, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France.
authors.forename: Guilhem
authors.initials: G
authors.lastname: Sempere
authors.affiliation: UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France.
authors.forename: Gautier
authors.initials: G
authors.lastname: Sarah
authors.affiliation: Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.
authors.forename: Yann
authors.initials: Y
authors.lastname: Hueber
authors.affiliation: UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Dufayard
authors.affiliation: 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.
authors.forename: Manuel
authors.initials: M
authors.lastname: Ruiz
mesh_terms: D014644:Genetic Variation; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D020407:Internet; D020641:Polymorphism, Single Nucleotide; D012984:Software