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SNiPlay, a web application for SNP analysis

Abstract : Sequencing and large scale genetic diversity projects have simultaneously increased in grapevine. As a consequence, the need to automatically detect polymorphisms and exploit subsequent sequence and genotyping data are growing accordingly. Here, we present SNiPlay, a web-based tool dedicated to SNP discovery and polymorphism analysis. It integrates a pipeline, freely accessible through the internet, combining existing software to compute different kinds of analysis. From allelic data, alignment, or sequencing traces given as input (notably using the Polymorfind program), it detects SNP and insertion/deletion events. Then it sends sequences and allelic data into an integrative pipeline able to achieve successive steps: - Mapping on the Vitis vinifera (‘Pinot’) reference genome and SNP annotation (genomic position, intron/exon, synonyme/non synonyme) ; - Haplotype reconstruction (using softwares Phase, Gevalt or ShapeIT); - Haplotype network (Haplophyle); - Linkage Disequilibrium (Haploview); - Diversity analysis (SeqLib library); It also includes a database to store polymorphism and genotyping data produced by projects on grapevine, notably SNPGrapeMap and DLVitis projects. Private access allows collaborators to explore data: SNP retrieval using various filters (genomic position, missing data, polymorphism type), comparison of SNPs between populations or other external information about accessions (geographical origin and phenotypic data), and export of genotype data in different formats. This database can collect and combine genotyping data coming from sequencing project as well as those obtained by Illumina chips and provides a section facilitating comparison between experiments. Finally, we plan to add a specific module able to manage and detect SNP from Next-Generation Sequencing data soon. Furthermore, SNiPlay is flexible enough to easily incorporate in the future new modules able to manage other kinds of analyses such as kinship, association studies, or population structure.
Mots-clés : GENETIQUE
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https://hal.inrae.fr/hal-02756324
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Submitted on : Wednesday, June 3, 2020 - 10:50:50 PM
Last modification on : Friday, October 8, 2021 - 4:26:35 PM

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  • HAL Id : hal-02756324, version 1
  • PRODINRA : 50200

Citation

Alexis Dereeper, Patrice This. SNiPlay, a web application for SNP analysis. 10. International Conference on Grapevine Breeding and Genetics, Aug 2010, Geneva (N.Y.), United States. ⟨hal-02756324⟩

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