Gigwa-Genotype investigator for genome-wide analyses.
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 that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats.



The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers.
UMR InterTryp (CIRAD), Campus International de Baillarguet, 34398, Montpellier, Cedex 5, France. guilhem.sempere@cirad.fr.|South Green Bioinformatics Platform, 1000 Avenue Agropolis, 34934, Montpellier, Cedex 5, France. guilhem.sempere@cirad.fr.
Guilhem
G
Sempéré
UMR DIADE (IRD), 911 Avenue Agropolis, 34934, Montpellier, Cedex 5, France.
Florian
F
Philippe
South Green Bioinformatics Platform, 1000 Avenue Agropolis, 34934, Montpellier, Cedex 5, France.|UMR IPME (IRD), 911 Avenue Agropolis, 34394, Montpellier, Cedex 5, France.
Alexis
A
Dereeper
South Green Bioinformatics Platform, 1000 Avenue Agropolis, 34934, Montpellier, Cedex 5, France.|UMR AGAP, CIRAD, 34398, Montpellier, Cedex 5, France.|Institut de Biologie Computationnelle, Université de Montpellier, 860 Rue de St Priest, 34095, Montpellier, Cedex 5, France.|Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), 6713, Cali, Colombia.
Manuel
M
Ruiz
South Green Bioinformatics Platform, 1000 Avenue Agropolis, 34934, Montpellier, Cedex 5, France.|INRA, UMR AGAP, 34398, Montpellier, Cedex 5, France.
Gautier
G
Sarah
South Green Bioinformatics Platform, 1000 Avenue Agropolis, 34934, Montpellier, Cedex 5, France.|UMR DIADE (IRD), 911 Avenue Agropolis, 34934, Montpellier, Cedex 5, France.|Institut de Biologie Computationnelle, Université de Montpellier, 860 Rue de St Priest, 34095, Montpellier, Cedex 5, France.|INRIA Zenith Team, LIRMM, 161 Rue Ada, 34095, Montpellier, Cedex 5, France.
Pierre
P
Larmande
D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D014644:Genetic Variation; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D016247:Information Storage and Retrieval; D020407:Internet; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
Genomic variations; HapMap; INDEL; MongoDB; NoSQL; SNP; VCF; Web interface