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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND BIOLOGICAL DETERMINANTS OF RESPIRATORY DISEASES OF RUMINANTS

Location: Genetics, Breeding, & Animal Health

Title: Enabling next-gen sequencing and analysis at the USDA-ARS U.S. Meat Animal Research Center with MiniLIMS

Authors
item Kitzmiller, Aaron -
item Clamp, Michele -
item Osborne, Brian -
item Zhang, Jiesheng -
item Smith, Timothy
item Harhay, Gregory

Submitted to: Advances in Genome Biology and Technology
Publication Type: Abstract Only
Publication Acceptance Date: December 7, 2011
Publication Date: N/A

Technical Abstract: There is a growing need to combine DNA sequencing technologies to address complex problems in genome biology. These genomic studies routinely generate voluminous image, sequence, and mapping files that should be associated with quality control information (gels, spectra, etc.), and other important sample metadata. Additionally, the volume and heterogeneity of next-gen and associated data creates severe strains on IT infrastructures. In the case of the USDA-ARS U.S. Meat Animal Research Center, BioTeam created customized hardware and software solutions that enabled capture and integration of 454 FLX+ and Pacific Bioscience RS sequencer data and metadata in the MiniLIMS environment. Traditional compute nodes were combined with large memory machines and high-performance networked storage to support annotation and assembly. The MiniLIMS platform provided an environment where data from multiple sources were associated with samples, libraries, and sequencing runs though a clean and flexible GUI interface, rapidly adapting to changes over the course of the project. MiniLIMS also provided key links between laboratory data and analysis results by launching software pipelines and collecting results (for example, microbial genome sequence assembly and annotation with the DIYA pipeline). DIYA provides a single annotation environment, facilitating the comparative genomics of in-house and downloaded sequences from public databases.

Last Modified: 4/17/2014
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