Easily manage, share, explore, visualize NGS genotyping data.
Support for VCF , Hapmap , PLINK formats, RESTful standards, Galaxy and FlapJack connectivity.


Gigwa helps managing, sharing, and exploring high density genotyping data (typically VCF files)

This project was funded by Agropolis Fondation under the reference ID ARCAD 0900-001.



The Agronomic Linked Data knowledge graph database for plant molecular data
Pierre Larmande

IBC - Institut de Biologie Computationnelle

IFB - Institut Francais de Bioinformatique

Cassava Genome Hub

the integrated portal for cassava
Manuel Ruiz, Alexis Dereeper

Agropolis Fondation (Twin post-doc)


The EURIGEN project "Genotyping for the Conservation and Valorization of European Rice Germplasm", is the Action 049 of the AGRI GEN RES program for conservation, characterisation, collection and utilization of genetic resources in agriculture funded by the European Commission - DG Agriculture and Rural Development. 

Eurigen Database manages genetic, phenotypic and genomic information on rice working collections of European institutions
Chantal Hamelin

European Commission - DG Agriculture and Rural Development

Cocoa Genome Hub

Access the cocoa Criollo Genome Version 2 with 99% of the genes anchored to the 10 chromosomes

a Web portal for crossing cocoa phenotypic, genetic and genomic data from ICGD and TropGeneDB databases
Gaëtan Droc

Banana Genome Hub

The Banana Genome Hub centralises databases of genetic and genomic data for the musa acuminata crop Hub developed by Cirad and Bioversity and supported by the South Green Bioinformatics platform. Data available are the complete genome sequence along with gene structure, gene product information, metabolism, gene families, transcriptomics (ESTs, RNA-Seq), genetic markers (SSR, DArT, SNPs) and genetic maps.

the integrated crop portal for Musa



TropGeneDB is a component of the South Green Bioinformatics Platform for the management of genetic, molecular and phenotypic data on tropical crop species. The most common data stored in TropGeneDB are molecular markers, QTLs (Quantitative Trait Loci), genetic and physical maps, genetic diversity, phenotypic diversity studies, and information on genetic resources (geographic origin, parentage, collection). TropGeneDB is organized on a crop basis with currently nine public modules (banana, cocoa, coconut, coffee, cotton, oil palm, rice, rubber tree, sugarcane).

gene database for tropical plants
Chantal Hamelin, Manuel Ruiz

This project is mainly supported by CIRAD core funding.


SNiPlay is a web-based tool for SNP and polymorphism analysis. From sequencing traces, alignment or allelic data given as input, it detects or extracts SNP and insertion/deletion events. In a second step, it sends sequences and allelic data into an integrative pipeline

SNP and polymorphism analysis
Alexis Dereeper

ANR DLVitis (2009), ANR GnpAsso (2012)

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