NG6


"The platform works in tight collaboration with the GeT sequencing platform for the management and the analysis of data produced by their Roche 454 and Illumina HiSeq sequencers. NG6 is an extensible sequencing provider oriented LIMS. It includes read quality control and first level analysis processes which ease the data validation made jointly by the sequencing facility staff ant the end-users. It provides a secured user-friendly interface to visualize and download the raw sequences files and the analysis results."

Background

Next generation sequencing platforms are now well implanted in sequencing centres and some laboratories. Upcoming smaller scale machines such as the 454 junior from Roche or the MiSeq from Illumina will increase the number of laboratories hosting a sequencer. In such a context, it is important to provide these teams with an easily manageable environment to store and process the produced reads.

 

Results

We describe a user-friendly information system able to manage large sets of sequencing data. It includes, on one hand, a workflow environment already containing pipelines adapted to different input formats (sff, fasta, fastq and qseq), different sequencers (Roche 454, Illumina HiSeq) and various analyses (quality control, assembly, alignment, diversity studies,…) and, on the other hand, a secured web site giving access to the results. The connected user will be able to download raw and processed data and browse through the analysis result statistics. The provided workflows can easily be modified or extended and new ones can be added. Ergatis is used as a workflow building, running and monitoring system. The analyses can be run locally or in a cluster environment using Sun Grid Engine.

 

Conclusions

NG6 is a complete information system designed to answer the needs of a sequencing platform. It provides a user-friendly interface to process, store and download high-throughput sequencing data.


Informations générales
Suivi
Maintenu
Informations spécifiques
Langage(s) de développement
N° de version courante
V2.0
Date de la version courante
OS supporté
Type de licence
GPL


Porteur(s)
Unité
MIAT
Equipe
PF Genotoul
Département co-porteur
GA
Auteur(s)
Jérôme Mariette
Céline Noirot
Claire Kuchly
Contact
jerome.mariette@inra.fr; celine.noirot@inra.fr
Publication de référence


 

 

Système d'information scientifique MIA classé par unité (UR, UMR)

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