%0 Journal Article
%9 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES
%A Dereeper, Alexis
%A Homa, F.
%A Andres, G.
%A Sempere, G.
%A Sarah, G.
%A Hueber, Yann
%A Dufayard, J. F.
%A Ruiz, M.
%T SNiPlay3 : a web-based application for exploration and large scale analyses of genomic variations
%D 2015
%L fdi:010064929
%G ENG
%J Nucleic Acids Research
%@ 0305-1048
%M ISI:000359772700046
%N W1
%P W295-W300
%R 10.1093/nar/gkv351
%U https://www.documentation.ird.fr/hor/fdi:010064929
%> https://www.documentation.ird.fr/intranet/publi/2015/09/010064929.pdf
%V 43
%W Horizon (IRD)
%X 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 gresequencing) 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.
%$ 020