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

Jean-Pierre A. Kocher | Zendy; Daniel Quest | Zendy; Patrick E. Duffy | Zendy; Michael A. Meiners | Zendy; Raymond M. Moore | Zendy; David A. Rider | Zendy; Asif Hossain | Zendy; Steven N. Hart | Zendy; Valentin Dinu | Zendy

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

Author(s) -

Jean-Pierre A. Kocher,

Daniel Quest,

Patrick E. Duffy,

Michael A. Meiners,

Raymond M. Moore,

David A. Rider,

Asif Hossain,

Steven N. Hart,

Valentin Dinu

Publication year - 2014

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btu137

Subject(s) - annotation , computer science , perl , java , unix , json , world wide web , information retrieval , database , software , programming language , artificial intelligence

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.

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