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Title: Supporting information for "Gigwa - Genotype Investigator for Genome Wide Analyses"      
dateReleased:
05-24-2016
privacy:
not applicable
aggregation:
instance of dataset
dateCreated:
05-24-2016
refinement:
curated
ID:
doi:10.5524/100199
creators:
Sempere, Guilhem
Philippe, Florian
Dereeper, Alexis
Ruiz, Manuel
Sarah, Gautier
Larmande, Pierre
availability:
available
types:
sequence
description:
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 V1.0 (sole web-application, Windows bundle, OSX bundle), and the material used for benchmarking (data as VCF and CSV+SQL, VCFtools scripts, MySQL stored procedures).
accessURL: https://doi.org/10.5524/100199
storedIn:
GigaScience Database
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
GigaDB
homePage: http://gigadb.org/
ID:
SCR:006565
name:
Giga Science Database

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