IBISA-GnpSeqNGS
IBISA-GnpSeqNGS is a project funded by GIS IBISA for one year in 2011. The goal of this project was to improve GnpIS information system and its sequence database module, to manage NGS data, such as genomic sequencing or resequencing data produced by 454, Illumina or HiSeq technologies. For each run, it is now possible to get a description of the sequencing experiment and an overview of the bioinformatics analyses performed. Interoperability with other modules of GnpIS gives access to more specific information, such as polymorphism detection analysis through the dedicated module GnpSNP.
Duration: 01/11/2010 to 31/12/2011
Coordinator: Delphine Steinbach
URGI platform was labellised by GIS IBISA and was the only member of this labellisation.
One position for one year was given: Célia Michotey is the main developper at URGI of this tool
The project was guided by URGI platform coordinator needs (Delphine Steinbach) and by community user needs taking into accounts NGS data that were already present at URGI or planned to arrive in the frame of other projects such as ANR GrapeReseq, ANR Muscares for Grape or ANR 3BSeq for Wheat.
Results:
- A simple submission file, with mandatory data in red, was created and a dedicated tool was developed with the ETL (Extract Transform and Load) Talend to allow automatic data insertion in GnpSeq NGS database.
- A module « sequence » was developed in Java and added to GnpIS’s web portal to access data stored in GnpSeq NGS.
- A series of search forms facilitates exhaustive or restricted queries and retrieval of NGS data from the database.
- The run card gather all representative information of a run: origin (experiment), analyses performed, sequence and other linked files. Some analyses tools, such as URGI’s Galaxy pipelines, are easily reachable for further data analysis.
- A poster will be presented at the next bioinformatics conference in Jobim 2012:
GnpSeq NGS: a new tool to manage NGS data in URGI’s information system (GnpIS) : Célia Michotey, Nacer Mohellibi, Hadi Quesneville and Delphine Steinbach, JOBIM Rennes July 2012.
Perspectives:
- GnpSeq NGS developments are closed.
- The tool is now ready to host data coming from other various NGS species projects running on the URGI platform and for future projects.
Software license: AGPLv3 (Affero General Public license version 3)
For interest in the sofware or question : please contact Delphine Steinbach at versailles.inra.fr
Creation date: 20 Jun 2012
eZ PublishPublication supervisor: A-F. Adam-Blondon
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