title: Galaxy LIMS for next-generation sequencing.
abstract: CONCLUSIONS
  We have developed a laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform. The system provides lab technicians standard and customizable sample information forms, barcoded submission forms, tracking of input sample quality, multiplex-capable automatic flow cell design and automatically generated sample sheets to aid physical flow cell preparation. In addition, the platform provides the researcher with a user-friendly interface to create a request, submit accompanying samples, upload sample quality measurements and access to the sequencing results. As the LIMS is within the Galaxy platform, the researcher has access to all Galaxy analysis tools and workflows. The system reports requests and associated information to a message queuing system, such that information can be posted and stored in external systems, such as a wiki. Through an API, raw sequencing results can be automatically pre-processed and uploaded to the appropriate request folder. Developed for the Illumina HiSeq 2000 instrument, many features are directly applicable to other instruments.
  
  
  METHODS
  The code and documentation are available at http://tron-mainz.de/tron-facilities/computational-medicine/galaxy-lims/
authors.affiliation: Computational Medicine, TRON - Translational Oncology at the Johannes Gutenberg University of Mainz Medicine, 55131 Mainz, Germany. jelle.scholtalbers@tron-mainz.de
authors.forename: Jelle
authors.initials: J
authors.lastname: Scholtalbers
authors.forename: Jasmin
authors.initials: J
authors.lastname: Rößler
authors.forename: Patrick
authors.initials: P
authors.lastname: Sorn
authors.forename: Jos
authors.initials: J
authors.lastname: de Graaf
authors.forename: Valesca
authors.initials: V
authors.lastname: Boisguérin
authors.forename: John
authors.initials: J
authors.lastname: Castle
authors.forename: Ugur
authors.initials: U
authors.lastname: Sahin
mesh_terms: D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D007256:Information Systems; D012984:Software; D014584:User-Computer Interface; D057188:Workflow