Supporting information for "Gigwa - Genotype Investigator for Genome Wide Analyses".
Dataset type: Software
Data released on May 24, 2016
Exploring the structure of genomes and analysing their evolution is essential to understand the ecological adaptation of organisms. However, with the large amounts of data being produced by Next Generation Sequencing (NGS), computational challenges arise in terms of storage, search, sharing, analysis, and visualisation. This is particularly true regarding genomic variation studies that 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.
The Gigwa application is suitable to manage large amounts of genomic variations through a user-friendly web interface making such a processing widely accessible. It may either be simply deployed on a workstation or used to provide a data portal to a given community of researchers.
Resources available here consist of the binary files for Gigwa V1.0beta (sole web-application, Windows bundle, OSX bundle), and the material used for benchmarking (data as VCF and CSV+SQL, VCFtools scripts, MySQL stored procedures).
Please visit Gigwa website for most recent updates to this software.
Read the peer-reviewed publication(s):
Sempéré, G., Philippe, F., Dereeper, A., Ruiz, M., Sarah, G., & Larmande, P. (2016). Gigwa—Genotype investigator for genome-wide analyses. GigaScience, 5(1). doi:10.1186/s13742-016-0131-8
There is a new version of this dataset available at: DOI: 10.5524/100585
Accessions (data referenced by this study):