South Green resources to manage Rice Big Genomics Data [W682]

Agret Clément, Gottin Celine, Dereeper Alexis, Tranchant-Dubreuil Christine, Chateau Annie, Diévart Anne, Sarah Gautier, Mancheron Alban, Sempere Guilhem, Ruiz Manuel, Droc Gaëtan. 2020. South Green resources to manage Rice Big Genomics Data [W682]. In : Abstracts workshops of the PAG XXVIII. San Diego : PAG, Résumé, 302. Plant and Animal Genome. 28, San Diego, États-Unis, 11 Janvier 2020/15 Janvier 2020.

Résumé : We have developed the Rice Genome Hub, an integrative genome information system that allows centralized access to genomics and genetics data, and analytical tools to facilitate translational and applied research in rice. The hub is built using the Content Management System Drupal with the Tripal module that interacts with the Chado database. The Hub interface provides several functionalities (Blast, DotPlots, Gene Search, JBrowse, Primer Blaster, Primer Designer) to make it easy for querying, visualizing and downloading research data. We also plugged in-house tools developed by the South Green bioinformatics platform. Among these tools, Gigwa is a Web-based tool which provides an easy and intuitive way to explore large amounts of genotyping data by filtering the latter based not only on variant features, including functional annotations, but also on genotype patterns. We also developed RedOak, a reference-free and alignment-free software package that allows for the indexing of a large collection of similar genomes. RedOak can be applied to reads from unassembled genomes, and it provides a nucleotide sequence query function. This software is based on a k-mer approach and has been developed to be heavily parallelized and distributed on several nodes of a cluster. Analysis of presence-absence variation (PAV) of genes among different genomes is a classical output of pan-genomic approaches. RedOak has a nucleotide sequence query function, including reverse complements, that can be used to quickly analyze the PAV of a specific gene among a large collection of genomes.

Auteurs et affiliations

• Agret Clément, CIRAD-BIOS-UMR AGAP (FRA)
• Gottin Celine, CIRAD-BIOS-UMR AGAP (FRA)
• Dereeper Alexis, CIRAD-BIOS-UMR AGAP (GLP)
• Tranchant-Dubreuil Christine, IRD (FRA)
• Chateau Annie, CNRS (FRA)
• Diévart Anne, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-9460-4638
• Sarah Gautier, INRA (FRA)
• Mancheron Alban, CNRS (FRA)
• Sempere Guilhem, CIRAD-BIOS-UMR INTERTRYP (FRA) ORCID: 0000-0001-7429-2091
• Ruiz Manuel, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-8153-276X
• Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-1849-1269

Source : Cirad-Agritrop (https://agritrop.cirad.fr/594769/)

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