The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation

Jean-Pierre A. Kocher, Daniel J. Quest, Patrick Duffy, Michael A. Meiners, Raymond M. Moore, David Rider, Asif Hossain, Steven N. Hart, Valentin Dinu
2014 Computer applications in the biosciences : CABIOS  
Motivation: The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined with
more » ... r UNIX commands for advanced annotation processing. We also provide instructions for the development of custom annotation pipelines. Availability and implementation: The package is implemented in Java and makes use of external tools written in Java and Perl. The toolkit can be executed on Mac OS X
doi:10.1093/bioinformatics/btu137 pmid:24618464 pmcid:PMC4071205 fatcat:x6dcfudyynfa5pqqnj4ba3sle4