Supporting information for "Gigwa - Genotype Investigator for Genome Wide Analyses".

Dataset type: Software
Data released on May 24, 2016

Dereeper A; Larmande P; Philippe F; Ruiz M; Sarah G; Sempere G (2016): Supporting information for "Gigwa - Genotype Investigator for Genome Wide Analyses". GigaScience Database. http://dx.doi.org/10.5524/100199

DOI10.5524/100199

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.

Additional details

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

Related datasets:

doi:10.5524/100199 References doi:10.5524/200001

Additional information:

http://www.southgreen.fr/content/gigwa

Accessions (data not in GigaDB):

BioProject: PRJEB6180





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Rice30004530RicericeOryza sativa Description:combination of 3000+ rice line sequences, see BioProject:PRJEB6180
Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Sequence variantsarchive19.28 MB2016-04-22
Sequence variantsarchive1.94 MB2016-04-22
Sequence variantsarchive212.99 KB2016-04-22
Sequence variantsarchive192.84 MB2016-04-22
Mixed archivearchive141.22 MB2016-04-22
Mixed archivearchive14.72 MB2016-04-22
Mixed archivearchive179.9 MB2016-04-22
ScriptUNKNOWN30.44 KB2016-04-22
Sequence variantsarchive290.03 MB2016-04-22
Sequence variantsarchive29.01 MB2016-04-22
Displaying 1-10 of 21 File(s).
Date Action
May 24, 2016 Dataset publish
June 10, 2016 Manuscript Link added : 10.1186/s13742-016-0131-8
July 1, 2016 Description updated from : 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).
July 1, 2016 File Gigwa_V1.0beta_Webapp.zip updated
July 1, 2016 File Gigwa_V1.0beta_OSX_Bundle.zip updated
July 1, 2016 File Gigwa_V1.0beta_Windows_Bundle.zip updated
April 4, 2017 Description updated from : 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).