Skip to Main content Skip to Navigation
Journal articles

NG6: Integrated next generation sequencing storage and processing environment.

Abstract : 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.
Document type :
Journal articles
Complete list of metadatas

Cited literature [13 references]  Display  Hide  Download

https://www.hal.inserm.fr/inserm-00733481
Contributor : Ed. Bmc <>
Submitted on : Tuesday, September 18, 2012 - 5:04:55 PM
Last modification on : Tuesday, July 21, 2020 - 3:22:02 PM
Long-term archiving on: : Wednesday, December 19, 2012 - 3:46:12 AM

Files

Identifiers

Collections

Citation

Jérôme Mariette, Frédéric Escudié, Nicolas Allias, Gérald Salin, Céline Noirot, et al.. NG6: Integrated next generation sequencing storage and processing environment.. BMC Genomics, BioMed Central, 2012, 13 (1), pp.462. ⟨10.1186/1471-2164-13-462⟩. ⟨inserm-00733481⟩

Share

Metrics

Record views

330

Files downloads

368