GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture

Hákon Guðbjartsson, Guðmundur Fr. Georgsson, Sigurjón A. Guðjónsson, Ragnar þór Valdimarsson, Jóhann H. Sigurðsson, Sigmar K. Stefánsson, Gísli Másson, Gísli Magnússon, Vilmundur Pálmason, Kári Stefánsson
2016 Bioinformatics  
Motivation: 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. Results: 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
more » ... patial overlap between various types of genomic features, filter and aggregate them in various ways. Availability and Implementation: The GORpipe software is freely available for non-commercial academic usage and can be downloaded from www.nextcode.com/
doi:10.1093/bioinformatics/btw199 pmid:27339714 pmcid:PMC5048061 fatcat:rxxgwarcorgidb2fo3go5chzly