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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.culebrONT
A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.GeMo
A mosaic genome painting tool for plant genomesVcfHunter
VcfExplorer regroups several programs which principal aims are to map DNA and RNAseq data onto reference genome sequence, perform variant calling, manipulate vcf files, perform chromosome painting of accessions based on the contribution of ancestral groups, select marker for genetic map analysis and perform pairwise chromosome linkage of ordered markers.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.Gigwa2
trainings
The South Green platform has conducted a series of training courses for several years and this github repository gives access to all trainings (https://southgreenplatform.github.io/trainings/).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.PanExplorer
Web application to explore bacterial pangenomesrap-green
Phylogenetic tree management, exploration and display packageUniqprimer
training_ONT_teaching
tutorials
An open resource material for people who wish to know about bioinformatics specially users of the Southgreen Platform (https://southgreenplatform.github.io/tutorials/). It contains tips, tutorials on bioinformatics analysis and softwares.galaxy-wrappers
Galaxy tools from South GreenPanExplorer_workflow
Snakemake worklow for bacterial pan-genome analysis. It can be run in the back-end of PanExplorer web applicationscaffhunter
Tools to order scaffolds into chromosomes based on genetic mapping datascaffremodler
Tools to correct genome assembly using NGS datatraining_reproducible_research
Training on Tools for Reproducible Research given by SouthGreenduplicationDetector
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.gigwa
Genotype Investigator for Genome Wide Analysestraining_python
Python training given by SouthGreen (https://southgreenplatform.github.io/training_python)training_bacterial_comparative_genomics
Trainings for Bacterial Comparative Genomics (https://southgreenplatform.github.io/training_bacterial_comparative_genomics/)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.documentation
Documentation related to the SouthGreen Platform - https://southgreenplatform.github.io/documentation/AgroLD_webappV2
New version of the AgroLD Web appMgdb2BrapiV2Impl
GeLoc
Geloc provides convenient tools to visualised and download LRR genes family annotation data.staff-info
Interactive SouthGreen Staff Information pagetraining_advanced_linux_and_bash_initiation
(https://southgreenplatform.github.io/training_advanced_linux_and_bash_initiation)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.Love Open Source and this site? Check out how you can help us