GCC 2017

➔ Slides

Authors

• Jean-François Dufayard, CIRAD UMR AGAP (AGAP)  
• Marilyne Summo, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)  
• Gaëtan Droc, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)  
• Mathieu Rouard, CIRAD UMR AGAP (AGAP)  
• Bertrand Pitollat, CIRAD UMR AGAP (AGAP)  
• Paul Pastor, CIRAD UMR AGAP (AGAP)  
• Delphine Larivière, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)  
• Frédéric De Lamotte, INRA UMR AGAP (AGAP)  
• Stéphanie Bocs, CIRAD UMR AGAP (AGAP)  
• Manuel Ruiz, CIRAD UMR AGAP (AGAP)  
• Felix Homa, CIRAD UMR AGAP (AGAP)  
• Guillaume Martin, CIRAD UMR AGAP (AGAP)  
• Gautier SARAH, Amélioration Génétique et Adaptation des Plantes Méditerranéeennes et Tropicales (AGAP)
• Sébastien RAVEL, Biologie et génétique des interactions plantes-parasites pour la protection intégrée (BGPI)
• Vincent Maillol, CIRAD UMR AGAP (AGAP)  
• Jonathan Lorenzo, Institut Français de Bioinformatique (IFB)   
• Alexis Dereeper, CIRAD UMR AGAP (AGAP)  

Abstract

South Green is a bioinformatics platform applied to the genomic resource analysis of southern and Mediterranean plants. The South Green web portal (http://www.southgreen.fr/) provides access to a large panel of bioinformatics resources including its own Galaxy instance which support a large community of users in Montpellier, France and beyond.

In addition to the generic tools provided with the standard installation of Galaxy, the South Green Galaxy instance (http://galaxy.southgreen.fr/galaxy/) contains a large collection of exclusive tools, Galaxy wrappers and workflows designed for analyses applied to plant genomes.

It actually comprises more than 100 Galaxy wrappers, 9 pre-configured workflows designed for recurrent analyses such as NGS mapping/cleaning, RNAseq, SNP calling and filtering, Genome-Wide Association Study, basic population genetics, structural variations, metagenomics and phylogenetics. We also developed innovative solution to graphically display outputs of each workflows.

Home-made Galaxy wrappers have been deposited in our local/central toolshed (http://galaxy.southgreen.fr/toolshed/) or in github (https://github.com/SouthGreenPlatform/galaxy-wrappers). Galaxy is extensively used to conduct capacity building activities. It is currently connected to HPC but we are also initiating use of Docker to disseminate some workflows in the IFB cloud, thus facilitating training activities worldwide.