title: GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture.
abstract: Our aim was to create a general-purpose relational data format and analysis tools to provide an efficient and coherent framework for working with large volumes of DNA sequence data.
  
  
  
  For this purpose we developed the GORpipe software system. It is based on a genomic ordered architecture and uses a declarative query language that combines features from SQL and shell pipe syntax in a novel manner. The system can for instance be used to annotate sequence variants, find genomic spatial overlap between various types of genomic features, filter and aggregate them in various ways.
  
  
  
  The GORpipe software is freely available for non-commercial academic usage and can be downloaded from www.nextcode.com/gorpipe CONTACT: hakon@wuxinextcode.comSupplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: WuXiNextCode Genomics, Sturlugata 8, 101 Reykjavík, Iceland.
authors.forename: Hákon
authors.initials: H
authors.lastname: Guðbjartsson
authors.affiliation: deCODE Genetics, Sturlugata 8, 101 Reykjavík, Iceland.
authors.forename: Guðmundur Fr
authors.initials: GF
authors.lastname: Georgsson
authors.affiliation: deCODE Genetics, Sturlugata 8, 101 Reykjavík, Iceland.
authors.forename: Sigurjón A
authors.initials: SA
authors.lastname: Guðjónsson
authors.affiliation: deCODE Genetics, Sturlugata 8, 101 Reykjavík, Iceland.
authors.forename: Ragnar Þór
authors.initials: RÞ
authors.lastname: Valdimarsson
authors.affiliation: WuXiNextCode Genomics, Sturlugata 8, 101 Reykjavík, Iceland.
authors.forename: Jóhann H
authors.initials: JH
authors.lastname: Sigurðsson
authors.affiliation: WuXiNextCode Genomics, Sturlugata 8, 101 Reykjavík, Iceland.
authors.forename: Sigmar K
authors.initials: SK
authors.lastname: Stefánsson
authors.affiliation: deCODE Genetics, Sturlugata 8, 101 Reykjavík, Iceland.
authors.forename: Gísli
authors.initials: G
authors.lastname: Másson
authors.affiliation: WuXiNextCode Genomics, Sturlugata 8, 101 Reykjavík, Iceland.
authors.forename: Gísli
authors.initials: G
authors.lastname: Magnússon
authors.affiliation: WuXiNextCode Genomics, Sturlugata 8, 101 Reykjavík, Iceland.
authors.forename: Vilmundur
authors.initials: V
authors.lastname: Pálmason
authors.affiliation: deCODE Genetics, Sturlugata 8, 101 Reykjavík, Iceland.
authors.forename: Kári
authors.initials: K
authors.lastname: Stefánsson
mesh_terms: D016678:Genome; D023281:Genomics; D017422:Sequence Analysis, DNA; D012984:Software