Open Access Highly Accessed Open Badges Software

NG6: Integrated next generation sequencing storage and processing environment

Jérôme Mariette1*, Frédéric Escudié2, Nicolas Allias1, Gérald Salin2, Céline Noirot1, Sylvain Thomas1 and Christophe Klopp1

Author Affiliations

1 Plate-forme bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France

2 Plate-forme genomique Genotoul, INRA, Génétique Cellulaire, BP 52627, 31326, Castanet-Tolosan Cedex, France

For all author emails, please log on.

BMC Genomics 2012, 13:462  doi:10.1186/1471-2164-13-462

Published: 9 September 2012



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.


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.


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.