Publications des scientifiques de l'IRD

Sempéré G., Philippe Florian, Dereeper Alexis, Ruiz M., Sarah G., Larmande Pierre. (2016). Gigwa - Genotype investigator for genome-wide analyses [+ erratum]. Gigascience, 5, art. 25 [9 p.+ erratum : vol. 5, art. no 48]. ISSN 2047-217X.

Titre du document
Gigwa - Genotype investigator for genome-wide analyses [+ erratum]
Année de publication
2016
Type de document
Article référencé dans le Web of Science WOS:000377153600001
Auteurs
Sempéré G., Philippe Florian, Dereeper Alexis, Ruiz M., Sarah G., Larmande Pierre
Source
Gigascience, 2016, 5, art. 25 [9 p.+ erratum : vol. 5, art. no 48] ISSN 2047-217X
Background: 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. Description: 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. Conclusions: 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.
Plan de classement
Sciences fondamentales / Techniques d'analyse et de recherche [020] ; Informatique [122]
Localisation
Fonds IRD [F B010066961]
Identifiant IRD
fdi:010066961
Contact