Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions.

Here we present Gigwa, a web-based tool which provides an easy and intuitive way to explore large amounts of genotyping data by filtering the latter based not only on variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability perspectives. Gigwa can handle multiple databases and may be deployed in either single or multi-user mode. Finally, it provides a wide range of popular export formats.



Try Gigwa v2 online with public datasets (or your own data!) at:


From v1.5 upwards, if you install the webapp on your own server you must log in as gigwadmin (password: nimda) to manage databases and user permissions. It is of course recommended to change the administrator password.

Gigwa installation archive (sole Java EE web-application)

v2.0-RELEASE (log in as gigwadmin / nimda after install)
v2.0-RC2 (log in as gigwadmin / nimda after install)
v2.0beta (log in as gigwadmin / nimda after install)
v2.0alpha (log in as gigwadmin / nimda after install)
v1.5 (log in as gigwadmin / nimda after install)


Bundled Gigwa archive for Windows 7+ (contains JRE, Apache Tomcat and MongoDB)
v2.0-RELEASEv2.0-RC2 - v2.0beta - v2.0alphav1.1 - v1.0beta

Bundled Gigwa archive for OSX 10.11+ (contains JRE, Apache Tomcat and MongoDB)
v2.0-RELEASEv2.0-RC2v2.0beta - v2.0alphav1.1 - v1.0beta

Bundled Gigwa archive for Ubuntu 16+ (contains JRE, Apache Tomcat and MongoDB)
v2.0-RELEASEv2.0-RC2 - v2.0beta


Release notes for published versions
Gigwa v1 administration guide (how to install and administrate a Gigwa instance from the above)
Gigwa v1 source code (for developers)
Gigwa v2 source code (for developers)


Video 1 - importing data (2'39) 
Video 2 - filtering data (3'57)
Video 3 - managing outputs (3'27)
Video 4 - phenotype-based discrimination (2'36)



Manuel Ruiz, Mathieu Rouard

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

Data types: 
Gene, Genotype, Marker, SNP