Dereeper Alexis, Homa F., Andres G., Sempere G., Sarah G., Hueber Yann, Dufayard J. F., Ruiz M. (2015). SNiPlay3 : a web-based application for exploration and large scale analyses of genomic variations. Nucleic Acids Research, 43 (W1), p. W295-W300. ISSN 0305-1048.
Titre du document
SNiPlay3 : a web-based application for exploration and large scale analyses of genomic variations
Dereeper Alexis, Homa F., Andres G., Sempere G., Sarah G., Hueber Yann, Dufayard J. F., Ruiz M.
Source
Nucleic Acids Research, 2015,
43 (W1), p. W295-W300 ISSN 0305-1048
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.
Plan de classement
Sciences fondamentales / Techniques d'analyse et de recherche [020]