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agrold_etl

AgroLD is a RDF knowledge base that consists of data integrated from a variety of plant resources and ontologies. AgroLD ETL is the Python packages developed to transform plant datasets in RDF. Packages are developped for data standards such as GFF,GAF, VCF and specific plant databases.

agrold_webapp

AgroLD is a RDF knowledge base that consists of data integrated from a variety of plant resources and ontologies. The aim of the Agronomic Linked Data (AgroLD) project is to provide a portal for bioinformatics and domain experts to exploit the homogenized data models towards efficiently generating research hypotheses.

arcad-hts

Scripts for the analysis of high-throughput sequencing data from the ARCAD project.

beegmac

culebront

A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.

curation-gbs-data

Coding data, filtering, correcting GE, (partial ) imputing, a

datalbase

daTALbase - Database for TAL Effectors analysis

dataviz

documentation

Documentation related to the SouthGreen Platform - https://southgreenplatform.github.io/documentation/

duplicationdetector

duplicationDetector is an accurate and very fast tool to easily and successfully detect duplicated genes or regions in any autogamous species. It relies on the abnormal number of heterozygous in a given interval for an autogamous (and thus highly homozygous) species.

galaxy

galaxy-docker-rnaseq

galaxy-wrappers

Galaxy tools from South Green

galaxyhomepage

galaxyhomepageird

geloc

Geloc provides convenient tools to visualised and download LRR genes family annotation data.

gemo

A mosaic genome painting tool for plant genomes

gigwa

Genotype Investigator for Genome Wide Analyses

gigwa2

metaxplor

Store, share, explore, manipulate metagenomic data

myrtaceae-rnaseq-scripts

panache

Panache is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show presence/absence information of pangenomic blocks of sequence or genes in a browser-like display.

panexplorer

Web application to explore bacterial pangenomes

panexplorer_workflow

Snakemake worklow for bacterial pan-genome analysis. It can be run in the back-end of PanExplorer web application

pathostdb

PathostDB is web-based database dedicated to Host-pathogen interactions in plants. It is a light interface that provides informations of resistance/sensibility to certain pathogens for given plants.

pyrice

PyRice is an API to access some Rice public databases at the same time with consistent output. PyRice design is modular and implements a smart query system which fits the computing resources to optimize the query speed.

rap-green

Phylogenetic tree management, exploration and display package

scaffhunter

Tools to order scaffolds into chromosomes based on genetic mapping data

scaffremodler

Tools to correct genome assembly using NGS data

singularityrecipefiles

This repository provides a series of Singularity recipe files used to easily deploy numerous bioinformatics softwares through containers.All these Singularity recipes are ready to be used by the bioinformatics community and have been developed to be integrated into the workflow manager TOGGLe http://toggle.southgreen.fr.