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

Alexis Dereeper, Felix Homa, Gwendoline Andres, Guilhem Sempere, Gautier Sarah, Yann Hueber, Jean-François Dufayard, Manuel Ruiz
2015 Nucleic Acids Research  
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
more » ... 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
doi:10.1093/nar/gkv351 pmid:26040700 pmcid:PMC4489301 fatcat:bwzcwxw53jgjbfqykr7rvgsf7m