Dereeper Alexis auteur aut IRD Homa F. auteur aut IRD Andres G. auteur aut IRD Sempere G. auteur aut IRD Sarah G. auteur aut IRD Hueber Yann auteur aut IRD Dufayard J. F. auteur aut IRD Ruiz M. auteur aut IRD text journalArticle eng text/pdf born digital access 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. specialized 020 43 W1 W295-W300 2015 0305-1048 https://www.documentation.ird.fr/hor/fdi:010064929 10.1093/nar/gkv351 0305-1048 [F B010064929] https://www.documentation.ird.fr/hor/fdi:010064929 https://www.documentation.ird.fr/intranet/publi/2015/09/010064929.pdf Accès réservé (Intranet de l'IRD) IRD - Base Horizon / Pleins textes 2015-10-07 2017-08-23 fdi:010064929 fre