Introduction

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 other 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 10.5 and above or any Linux distribution. The BioR application, quickstart, and user guide documents and many biological examples are available at http://bioinformaticstools.mayo.edu.

Publications

  1. The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.
    Cite this
    Kocher JP, Quest DJ, Duffy P, Meiners MA, Moore RM, Rider D, Hossain A, Hart SN, Dinu V, 2014-07-01 - Bioinformatics (Oxford, England)

Credits

  1. Jean-Pierre A Kocher
    Developer

    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, United States of America

  2. Daniel J Quest
    Developer

    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, United States of America

  3. Patrick Duffy
    Developer

    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, United States of America

  4. Michael A Meiners
    Developer

    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, United States of America

  5. Raymond M Moore
    Developer

    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, United States of America

  6. David Rider
    Developer

    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, United States of America

  7. Asif Hossain
    Developer

    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, United States of America

  8. Steven N Hart
    Developer

    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, United States of America

  9. Valentin Dinu
    Investigator

    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, United States of America

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Summary
AccessionBT000102
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByValentin Dinu