NG6: Integrated next generation sequencing storage and processing environment

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 pr...

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Bibliographic Details
Published in:	BMC genomics Vol. 13; no. 1; p. 462
Main Authors:	Mariette, Jérôme, Escudié, Frédéric, Allias, Nicolas, Salin, Gérald, Noirot, Céline, Thomas, Sylvain, Klopp, Christophe
Format:	Journal Article
Language:	English
Published:	England BioMed Central Ltd 09-09-2012 BioMed Central BMC
Subjects:	Applications software Biochemistry, Molecular Biology Data processing DNA sequencing Genomics Information systems Life Sciences Nucleotide sequencing Quality control Running Sequence Analysis, DNA Software Statistical analysis Sun Technology application User-Computer Interface France data management ngs ng6 next generation sequencing
Online Access:	Get full text
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 ObjectType-Article-2 ObjectType-Feature-1
ISSN:	1471-2164 1471-2164
DOI:	10.1186/1471-2164-13-462