SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations

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dc.creatorDereeper, Alexis
dc.creatorHoma, Felix
dc.creatorAndres, Gwendoline
dc.creatorSempéré, Guilhem
dc.creatorSarah, Gautier
dc.creatorHueber, Yann
dc.creatorDufayard, Jean-François
dc.creatorRuíz, Manuel
dc.date2015-07-01
dc.date2015-07-27T21:19:04Z
dc.date2015-07-27T21:19:04Z
dc.date.accessioned2026-06-27T14:30:21Z
dc.descriptionSNiPlay 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.
dc.identifierhttps://hdl.handle.net/10568/67422
dc.identifier.urihttp://hdl.handle.net/123456789/80151
dc.languageen
dc.publisherOxford University Press
dc.rightsOpen Access
dc.sourceDereeper, 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.
dc.subjectgenetic variation
dc.subjectdata analysis
dc.subjectcomputer applications
dc.subjectdatabases
dc.subjectgenetic polymorphism
dc.subjectgenotypes
dc.subjectgenomes
dc.subjectvariación genetica
dc.subjectanálisis de datos
dc.subjectaplicaciones del ordenador
dc.subjectbases de datos
dc.subjectpolimorfismo genético
dc.subjectgenotipos
dc.subjectgenomas
dc.subjectgenetics
dc.titleSNiPlay3: a web-based application for exploration and large scale analyses of genomic variations
dc.typeJournal Article

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Centro Internacional de Agricultura Tropical (CIAT)