SouthGreenPlatform/panache

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Created over 3 years ago
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SouthGreenPlatform/panache

SouthGreenPlatform

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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.

TOGGLE

Toolbox for generic NGS analyses - A framework to quickly build pipelines and to perform large-scale NGS analysis

GeMo

A mosaic genome painting tool for plant genomes

VcfHunter

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.

Jupyter Notebook

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 pangenomes

rap-green

Phylogenetic tree management, exploration and display package

Uniqprimer

training_ONT_teaching

Jupyter Notebook

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 Green

PanExplorer_workflow

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

scaffhunter

Tools to order scaffolds into chromosomes based on genetic mapping data

scaffremodler

Tools to correct genome assembly using NGS data

training_reproducible_research

Training on Tools for Reproducible Research given by SouthGreen

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.

gigwa

Genotype Investigator for Genome Wide Analyses

training_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/)

Jupyter Notebook

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 app

Mgdb2BrapiV2Impl

GeLoc

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

staff-info

Interactive SouthGreen Staff Information page

training_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.