PMID- 23479349
OWN - NLM
STAT- MEDLINE
DCOM- 20131028
LR  - 20181202
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Linking)
VI  - 29
IP  - 9
DP  - 2013 May 1
TI  - Galaxy LIMS for next-generation sequencing.
PG  - 1233-4
LID - 10.1093/bioinformatics/btt115 [doi]
AB  - SUMMARY: 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. AVAILABILITY AND 
      IMPLEMENTATION: The code and documentation are available at 
      http://tron-mainz.de/tron-facilities/computational-medicine/galaxy-lims/
FAU - Scholtalbers, Jelle
AU  - Scholtalbers J
AD  - Computational Medicine, TRON - Translational Oncology at the Johannes Gutenberg 
      University of Mainz Medicine, 55131 Mainz, Germany. 
      jelle.scholtalbers@tron-mainz.de
FAU - Rossler, Jasmin
AU  - Rossler J
FAU - Sorn, Patrick
AU  - Sorn P
FAU - de Graaf, Jos
AU  - de Graaf J
FAU - Boisguerin, Valesca
AU  - Boisguerin V
FAU - Castle, John
AU  - Castle J
FAU - Sahin, Ugur
AU  - Sahin U
LA  - eng
PT  - Journal Article
DEP - 20130311
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
SB  - IM
MH  - High-Throughput Nucleotide Sequencing/*methods
MH  - *Information Systems
MH  - *Software
MH  - User-Computer Interface
MH  - Workflow
EDAT- 2013/03/13 06:00
MHDA- 2013/10/29 06:00
CRDT- 2013/03/13 06:00
PHST- 2013/03/13 06:00 [entrez]
PHST- 2013/03/13 06:00 [pubmed]
PHST- 2013/10/29 06:00 [medline]
AID - btt115 [pii]
AID - 10.1093/bioinformatics/btt115 [doi]
PST - ppublish
SO  - Bioinformatics. 2013 May 1;29(9):1233-4. doi: 10.1093/bioinformatics/btt115. Epub 
      2013 Mar 11.