Gigwa
Easily manage, share, explore, visualize NGS genotyping data.
Gigwa supports multiple import/export formats, RESTful standards ( BrAPI & GA4GH ), SNiPlay , Galaxy and Flapjack connectivity.
Recent releases:
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offer real-time statistical graph calculation & display (MAF, Fst, Tajima's D);
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embed online versions of Flapjack-Bytes and IGV.js , allowing for smooth and convenient data exploration;
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feature a simple yet powerful interface to let data owners dump / restore databases (use it to avoid loosing data!)
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.
LIVE INSTANCES
Try the latest version online with public datasets (or play your own data!) at:
- CIRAD instance: https://gigwa.southgreen.fr/ (various species data)
- Bioversity Intl instance: https://www.crop-diversity.org/gigwa/ (Musa data)
- IRD instance: https://gigwa.ird.fr/ (Rice and Human data)
IMPORTANT NOTE
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 Docker container
As the image is on a Dockerhub repository , the only required file for running the container is the docker-compose file (always get the latest version!)
Important notice: Upgrading an existing Docker container from versions prior to v2.5 r equires running a preliminary script, please refer to https://github.com/SouthGreenPlatform/Gigwa2/issues/41
Gigwa webapp installation archive (sole Java EE web-application, no Tomcat, no MongoDB here)
v2.8-RELEASE (log in as gigwadmin / nimda after install)
v2.7-RELEASE (log in as gigwadmin / nimda after install)
v2.6.1-RELEASE (log in as gigwadmin / nimda after install)
v2.6-RELEASE (log in as gigwadmin / nimda after install)
v2.5.1-RELEASE (log in as gigwadmin / nimda after install)
v2.5-RELEASE (log in as gigwadmin / nimda after install)
v2.4.1-RELEASE (log in as gigwadmin / nimda after install)
v2.3-RELEASE (log in as gigwadmin / nimda after install)
v2.2-RELEASE (log in as gigwadmin / nimda after install)
v2.1-RELEASE (log in as gigwadmin / nimda after install)
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)
v1.1
Important notice: Webapp upgrade is supported via an "updateGigwa" script available for all 3 supported systems. Be sure to always use the latest version of the script (embedded in the webapp archive from v2.5)
Bundled Gigwa archive for Windows 7+ 64bit (contains JRE, Apache Tomcat and MongoDB)
v2.8-RELEASE (creation script) - v2.7-RELEASE (creation script) - v2.6.1-RELEASE - v2.6-RELEASE - v2.5.1-RELEASE - v2.5-RELEASE - v2.4.1-RELEASE - v2.3-RELEASE - v2.2-RELEASE - v2.1-RELEASE - v2.0-RELEASE - v2.0-RC2 - v2.0beta - v2.0alpha - v1.1 - v1.0beta
(log in as gigwadmin / nimda after install)
Bundled Gigwa archive for OSX 10.11+ (contains JRE, Apache Tomcat and MongoDB)
v2.8-RELEASE (creation script) - v2.7-RELEASE (creation script) - v2.6.1-RELEASE - v2.6-RELEASE - v2.5-1-RELEASE - v2.5-RELEASE - v2.4.1-RELEASE - v2.3-RELEASE - v2.2-RELEASE - v2.1-RELEASE - v2.0-RELEASE - v2.0-RC2 - v2.0beta - v2.0alpha - v1.1 - v1.0beta
(log in as gigwadmin / nimda after install)
OSX users must be aware of this
Bundled Gigwa archive for Ubuntu 18+ (contains JRE, Apache Tomcat and MongoDB)
v2.8-RELEASE (creation script) - v2.7-RELEASE (creation script) - v2.6.1-RELEASE - v2.6-RELEASE - v2.5.1-RELEASE - v2.5-RELEASE - v2.4.1-RELEASE - v2.3-RELEASE - v2.2-RELEASE
(log in as gigwadmin / nimda after install)
Bundled Gigwa archive for Ubuntu 16+ (contains JRE, Apache Tomcat and MongoDB)
v2.1-RELEASE - v2.0-RELEASE - v2.0-RC2 - v2.0beta
(log in as gigwadmin / nimda after install)
RELATED LINKS
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 DEMOS FOR GIGWA V2.0
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)
TUTORIALS:
Online building and visualization of neighbor-joining trees, from Gigwa SNP data
USEFUL TIPS:
This project was funded by Agropolis Fondation under the reference ID ARCAD 0900-001.
