title: NG6: Integrated next generation sequencing storage and processing environment.
abstract: 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.
authors.affiliation: Plate-forme bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France. Jerome.Mariette@toulouse.inra.fr
authors.forename: Jérôme
authors.initials: J
authors.lastname: Mariette
authors.forename: Frédéric
authors.initials: F
authors.lastname: Escudié
authors.forename: Nicolas
authors.initials: N
authors.lastname: Allias
authors.forename: Gérald
authors.initials: G
authors.lastname: Salin
authors.forename: Céline
authors.initials: C
authors.lastname: Noirot
authors.forename: Sylvain
authors.initials: S
authors.lastname: Thomas
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
mesh_terms: D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface