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Gigwa v2-Extended and improved genotype investigator.
Sempéré, Guilhem; Pétel, Adrien; Rouard, Mathieu; Frouin, Julien; Hueber, Yann; De Bellis, Fabien; Larmande, Pierre.
Afiliación
  • Sempéré G; Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR INTERTRYP, F-34398 Montpellier, France.
  • Pétel A; South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.
  • Rouard M; INTERTRYP, Univ Montpellier, CIRAD, Institut de Recherche pour le Développpement (IRD), Montpellier, France.
  • Frouin J; South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.
  • Hueber Y; DIADE, Univ Montpellier, IRD, 911 Avenue Agropolis, 34394 Montpellier, France.
  • De Bellis F; South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.
  • Larmande P; Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.
Gigascience ; 8(5)2019 05 01.
Article en En | MEDLINE | ID: mdl-31077313
BACKGROUND: The study of genetic variations is the basis of many research domains in biology. From genome structure to population dynamics, many applications involve the use of genetic variants. The advent of next-generation sequencing technologies led to such a flood of data that the daily work of scientists is often more focused on data management than data analysis. This mass of genotyping data poses several computational challenges in terms of storage, search, sharing, analysis, and visualization. While existing tools try to solve these challenges, few of them offer a comprehensive and scalable solution. RESULTS: Gigwa v2 is an easy-to-use, species-agnostic web application for managing and exploring high-density genotyping data. It can handle multiple databases and may be installed on a local computer or deployed as an online data portal. It supports various standard import and export formats, provides advanced filtering options, and offers means to visualize density charts or push selected data into various stand-alone or online tools. It implements 2 standard RESTful application programming interfaces, GA4GH, which is health-oriented, and BrAPI, which is breeding-oriented, thus offering wide possibilities of interaction with third-party applications. The project home page provides a list of live instances allowing users to test the system on public data (or reasonably sized user-provided data). CONCLUSIONS: This new version of Gigwa provides a more intuitive and more powerful way to explore large amounts of genotyping data by offering a scalable solution to search for genotype patterns, functional annotations, or more complex filtering. Furthermore, its user-friendliness and interoperability make it widely accessible to the life science community.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Biología Computacional / Genómica / Genotipo Límite: Humans Idioma: En Revista: Gigascience Año: 2019 Tipo del documento: Article País de afiliación: Francia Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Biología Computacional / Genómica / Genotipo Límite: Humans Idioma: En Revista: Gigascience Año: 2019 Tipo del documento: Article País de afiliación: Francia Pais de publicación: Estados Unidos