ArticleNucleic acids research2015
SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
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- VCF2Dis: an ultra-fast and efficient tool to calculate pairwise genetic distance and construct population phylogeny from VCF files.GigaScience · 2025Article
- High-Throughput Short Sequence Typing Schemes forMicroorganisms · 2023Article
- Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks.Plants (Basel, Switzerland) · 2023Article
- Genomic and Bioinformatic Resources for Perennial Fruit Species.Current genomics · 2022Review
- Nisin Mutant Prevention Concentration and the Role of Subinhibitory Concentrations on Resistance Development by Diabetic FootAntibiotics (Basel, Switzerland) · 2022Article
- Balancing selection at the human salivary agglutinin gene (iScience · 2022Article
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- A cluster of Ankyrin and Ankyrin-TPR repeat genes is associated with panicle branching diversity in rice.PLoS genetics · 2021Article
- Genetic control of flowering in greater yam (Dioscorea alata L.).BMC plant biology · 2021Article
- Genomic and Phenotypic Diversity of Cultivated and Wild Tomatoes with Varying Levels of Heat Tolerance.Genes · 2021Article
- ADMIXPIPE: population analyses in ADMIXTURE for non-model organisms.BMC bioinformatics · 2020Article
- SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat.GigaScience · 2020Article
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- Rice Galaxy: an open resource for plant science.GigaScience · 2019Article
- Gigwa v2-Extended and improved genotype investigator.GigaScience · 2019Article
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Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.