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

doi:10.1093/bioinformatics/btu137

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

Research output: Contribution to journal › Article › peer-review

43 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	1920-1922
Number of pages	3
Journal	Bioinformatics
Volume	30
Issue number	13
DOIs	https://doi.org/10.1093/bioinformatics/btu137
State	Published - Jul 1 2014

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btu137

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abstract = "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.",

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AU - Quest, Daniel J.

AU - Duffy, Patrick

AU - Meiners, Michael A.

AU - Moore, Raymond M.

AU - Rider, David

AU - Hossain, Asif

AU - Hart, Steven N.

AU - Dinu, Valentin

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ER -

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

Abstract

ASJC Scopus subject areas

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