SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations.
Bottom Line: 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.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.
Affiliation: UMR Interaction Plante-Microorganismes et Environnement (IPME), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France email@example.com.Show MeSH
Mentions: GWAS have proven a useful technique for identifying genetic loci involved in the control of agronomic traits. Using an efficient implementation of softwares devoted to GWAS, including TASSEL (20) (General Linear Model (GLM) or Mixed Linear Model (MLM) methods) or MLMM (Multi-Locus Mixed Model) R package (21), phenotypic values of traits can be uploaded and mapped with an accurate model in order to estimate causal variants. This module offers a user-friendly interface that includes interactive Manhattan plots of association P-values along the chromosomes, as well as the QQ-plots commonly used for GWAS to show the importance of correcting for population structure and kinship information (Figure 3).
Affiliation: UMR Interaction Plante-Microorganismes et Environnement (IPME), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France firstname.lastname@example.org.