Gigwa—Genotype investigator for genomewide analyses
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...
| Main Authors: | , , , , , |
|---|---|
| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Oxford University Press
2016
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/75712 |
| _version_ | 1855532525937491968 |
|---|---|
| author | Sempéré, Guilhem Philippe, Florian Dereeper, Alexis Ruíz, Manuel Sarah, Gautier Larmande, Pierre |
| author_browse | Dereeper, Alexis Larmande, Pierre Philippe, Florian Ruíz, Manuel Sarah, Gautier Sempéré, Guilhem |
| author_facet | Sempéré, Guilhem Philippe, Florian Dereeper, Alexis Ruíz, Manuel Sarah, Gautier Larmande, Pierre |
| author_sort | Sempéré, Guilhem |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace75712 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2016 |
| publishDateRange | 2016 |
| publishDateSort | 2016 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace757122025-03-13T09:44:44Z Gigwa—Genotype investigator for genomewide analyses Sempéré, Guilhem Philippe, Florian Dereeper, Alexis Ruíz, Manuel Sarah, Gautier Larmande, Pierre genomics databases computer applications genetic resources data analysis genómica bases de datos aplicaciones del ordenador recursos genéticos análisis de datos 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. 2016-12 2016-06-13T16:28:05Z 2016-06-13T16:28:05Z Journal Article https://hdl.handle.net/10568/75712 en Open Access image/jpeg Oxford University Press Sempéré, Guilhem; Philippe, Florian; Dereeper, Alexis; Ruiz, Manuel; Sarah, Gautier; Larmande, Pierre. 2016. Gigwa—Genotype investigator for genomewide analyses. GigaScience . BioMed Central Ltd., 5: 36. |
| spellingShingle | genomics databases computer applications genetic resources data analysis genómica bases de datos aplicaciones del ordenador recursos genéticos análisis de datos Sempéré, Guilhem Philippe, Florian Dereeper, Alexis Ruíz, Manuel Sarah, Gautier Larmande, Pierre Gigwa—Genotype investigator for genomewide analyses |
| title | Gigwa—Genotype investigator for genomewide analyses |
| title_full | Gigwa—Genotype investigator for genomewide analyses |
| title_fullStr | Gigwa—Genotype investigator for genomewide analyses |
| title_full_unstemmed | Gigwa—Genotype investigator for genomewide analyses |
| title_short | Gigwa—Genotype investigator for genomewide analyses |
| title_sort | gigwa genotype investigator for genomewide analyses |
| topic | genomics databases computer applications genetic resources data analysis genómica bases de datos aplicaciones del ordenador recursos genéticos análisis de datos |
| url | https://hdl.handle.net/10568/75712 |
| work_keys_str_mv | AT sempereguilhem gigwagenotypeinvestigatorforgenomewideanalyses AT philippeflorian gigwagenotypeinvestigatorforgenomewideanalyses AT dereeperalexis gigwagenotypeinvestigatorforgenomewideanalyses AT ruizmanuel gigwagenotypeinvestigatorforgenomewideanalyses AT sarahgautier gigwagenotypeinvestigatorforgenomewideanalyses AT larmandepierre gigwagenotypeinvestigatorforgenomewideanalyses |