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Data released on May 24, 2016

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

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 RIS BibTeX Text

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.

Contact Submitter

Related manuscripts:

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

Keywords:

Genomic variations VCF HapMap NoSQL MongoDB SNP INDEL web interface 

Software

http://gigadb.org/images/data/cropped/100199.png

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

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).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
Mixed archivearchive14.72 MB2016-04-22
Mixed archivearchive179.9 MB2016-04-22
Mixed archivearchive141.22 MB2016-04-22
ReadmeTEXT2.28 KB2016-04-25
ScriptUNKNOWN0.2 KB2016-04-22
ScriptUNKNOWN37.42 KB2016-04-22
ScriptUNKNOWN0.25 KB2016-04-22
ScriptUNKNOWN30.44 KB2016-04-22
ScriptUNKNOWN0.2 KB2016-04-22
ScriptUNKNOWN0.2 KB2016-04-22
Displaying 1-10 of 21 File(s).

History:

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