South Green Bioinformatics platform
Public repository of code for bioinformatics applications developed in the South Green Bioinformatics platform
Montpellier
Pinned Repositories
culebrONT
A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.
GeMo
A mosaic genome painting tool for plant genomes
Gigwa2
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.
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
TOGGLE
Toolbox for generic NGS analyses - A framework to quickly build pipelines and to perform large-scale NGS analysis
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/).
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.
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.
South Green Bioinformatics platform's Repositories
SouthGreenPlatform/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.
SouthGreenPlatform/culebrONT
A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.
SouthGreenPlatform/GeMo
A mosaic genome painting tool for plant genomes
SouthGreenPlatform/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.
SouthGreenPlatform/Gigwa2
SouthGreenPlatform/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/).
SouthGreenPlatform/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.
SouthGreenPlatform/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.
SouthGreenPlatform/PanExplorer
Web application to explore bacterial pangenomes
SouthGreenPlatform/rap-green
Phylogenetic tree management, exploration and display package
SouthGreenPlatform/training_ONT_teaching
SouthGreenPlatform/PanExplorer_workflow
Snakemake worklow for bacterial pan-genome analysis. It can be run in the back-end of PanExplorer web application
SouthGreenPlatform/training_reproducible_research
Training on Tools for Reproducible Research given by SouthGreen
SouthGreenPlatform/training_bacterial_comparative_genomics
Trainings for Bacterial Comparative Genomics (https://southgreenplatform.github.io/training_bacterial_comparative_genomics/)
SouthGreenPlatform/training_python
Python training given by SouthGreen (https://southgreenplatform.github.io/training_python)
SouthGreenPlatform/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.
SouthGreenPlatform/documentation
Documentation related to the SouthGreen Platform - https://southgreenplatform.github.io/documentation/
SouthGreenPlatform/GeLoc
Geloc provides convenient tools to visualised and download LRR genes family annotation data.
SouthGreenPlatform/staff-info
Interactive SouthGreen Staff Information page
SouthGreenPlatform/training_advanced_linux_and_bash_initiation
(https://southgreenplatform.github.io/training_advanced_linux_and_bash_initiation)
SouthGreenPlatform/Curation-GBS-data
Coding data, filtering, correcting GE, (partial ) imputing, a
SouthGreenPlatform/Myrtaceae-RNASeq-scripts
SouthGreenPlatform/beegmac
SouthGreenPlatform/DataViz
SouthGreenPlatform/Galaxy-docker-rnaseq
SouthGreenPlatform/metaXplor
Store, share, explore, manipulate metagenomic data
SouthGreenPlatform/training_ONT_VM
SouthGreenPlatform/training_SV_teaching
Training Detection of SNP and Structural Variants using short and long reads
SouthGreenPlatform/training_SV_VM
App TrainingSV: Biosphere BASE environment for SV analysis using Jupyter
SouthGreenPlatform/Workflow-snakemake-capture