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

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.

Bibliographic Details

Main Authors:	Dereeper, Alexis, Homa, Félix, Andres, Gwendoline, Sempere, Guilhem, Sarah, Gautier, Hueber, Yann, Dufayard, Jean François, Ruiz, Manuel
Format:	article biblioteca
Language:	eng
Subjects:	F30 - Génétique et amélioration des plantes, polymorphisme génétique, variation génétique, génome, bioinformatique, stratification de densité, banque de données, génotype, polymorphisme à nucléotide unique, application des ordinateurs, logiciel, http://aims.fao.org/aos/agrovoc/c_24031, http://aims.fao.org/aos/agrovoc/c_15975, http://aims.fao.org/aos/agrovoc/c_3224, http://aims.fao.org/aos/agrovoc/c_37958, http://aims.fao.org/aos/agrovoc/c_5eb4922f, http://aims.fao.org/aos/agrovoc/c_24833, http://aims.fao.org/aos/agrovoc/c_3225, http://aims.fao.org/aos/agrovoc/c_0273c413, http://aims.fao.org/aos/agrovoc/c_24009, http://aims.fao.org/aos/agrovoc/c_24008,
Online Access:	http://agritrop.cirad.fr/577746/ http://agritrop.cirad.fr/577746/7/577746.pdf
Tags:	Add Tag No Tags, Be the first to tag this record!