The Biological Reference Repository (BioR)

A rapid and flexible system for genomics annotation

Jean-Pierre Kocher, Daniel J. Quest, Patrick Duffy, Michael A. Meiners, Raymond M. Moore, David Rider, Asif Hossain, Steven Hart, Valentin Dinu

Research output: Contribution to journalArticle

28 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)1920-1922
Number of pages3
JournalBioinformatics
Volume30
Issue number13
DOIs
StatePublished - Jul 1 2014

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UNIX
Genomics
Repository
Annotation
Pipelines
Processing
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ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Kocher, J-P., Quest, D. J., Duffy, P., Meiners, M. A., Moore, R. M., Rider, D., ... Dinu, V. (2014). The Biological Reference Repository (BioR): A rapid and flexible system for genomics annotation. Bioinformatics, 30(13), 1920-1922. https://doi.org/10.1093/bioinformatics/btu137

The Biological Reference Repository (BioR) : A rapid and flexible system for genomics annotation. / Kocher, Jean-Pierre; Quest, Daniel J.; Duffy, Patrick; Meiners, Michael A.; Moore, Raymond M.; Rider, David; Hossain, Asif; Hart, Steven; Dinu, Valentin.

In: Bioinformatics, Vol. 30, No. 13, 01.07.2014, p. 1920-1922.

Research output: Contribution to journalArticle

Kocher, J-P, Quest, DJ, Duffy, P, Meiners, MA, Moore, RM, Rider, D, Hossain, A, Hart, S & Dinu, V 2014, 'The Biological Reference Repository (BioR): A rapid and flexible system for genomics annotation', Bioinformatics, vol. 30, no. 13, pp. 1920-1922. https://doi.org/10.1093/bioinformatics/btu137
Kocher, Jean-Pierre ; Quest, Daniel J. ; Duffy, Patrick ; Meiners, Michael A. ; Moore, Raymond M. ; Rider, David ; Hossain, Asif ; Hart, Steven ; Dinu, Valentin. / The Biological Reference Repository (BioR) : A rapid and flexible system for genomics annotation. In: Bioinformatics. 2014 ; Vol. 30, No. 13. pp. 1920-1922.
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