Sempere Guilhem, Larmande Pierre, Rouard Mathieu.
2022. Managing high-density genotyping data with Gigwa.
In : Plant Bioinformatics: methods and protocols. Edwards David (ed.)
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Version post-print
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Résumé : Next generation sequencing technologies enabled high-density genotyping for large numbers of samples. Nowadays SNP calling pipelines produce up to millions of such markers, but which need to be filtered in various ways according to the type of analyses. One of the main challenges still lies in the management of an increasing volume of genotyping files that are difficult to handle for many applications. Here, we provide a practical guide for efficiently managing large genomic variation data using Gigwa, a user-friendly, scalable and versatile application that may be deployed either remotely on web servers or on a local machine.
Mots-clés libres : NoSQL database, SNP markers, INDELs, VCF, Web tool, Interoperability
Auteurs et affiliations
- Sempere Guilhem, CIRAD-BIOS-UMR INTERTRYP (FRA)
- Larmande Pierre, IRD (FRA)
- Rouard Mathieu, Bioversity International (ITA)
Autres liens de la publication
Source : Cirad-Agritrop (https://agritrop.cirad.fr/600320/)
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