South Green Bioinformatics platform

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 genomes

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/).

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.

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

galaxy-wrappers

Galaxy tools from South Green

training_ONT_teaching

training_reproducible_research

Training on Tools for Reproducible Research given by SouthGreen

PanExplorer_workflow

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

training_bacterial_comparative_genomics

Trainings for Bacterial Comparative Genomics (https://southgreenplatform.github.io/training_bacterial_comparative_genomics/)

training_python

Python training given by SouthGreen (https://southgreenplatform.github.io/training_python)

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.

documentation

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

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)

Curation-GBS-data

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

Myrtaceae-RNASeq-scripts

beegmac

DataViz

Galaxy-docker-rnaseq

metaXplor

Store, share, explore, manipulate metagenomic data

training_ONT_VM

training_SV_VM

App TrainingSV: Biosphere BASE environment for SV analysis using Jupyter

Workflow-snakemake-capture