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

Dereeper Alexis, Homa Félix, 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.

https://doi.org/10.1093/nar/gkv351

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Quartile : Outlier, Sujet : BIOCHEMISTRY & MOLECULAR BIOLOGY

Résumé : 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.

Mots-clés Agrovoc : polymorphisme génétique, variation génétique, génome, bioinformatique, stratification de densité, banque de données, génotype, polymorphisme à nucléotide unique, application des ordinateurs, logiciel

Classification Agris : F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : Hors axes (2014-2018)

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