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Bioinformatics. 2016 Oct 15;32(20):3081-3088. Epub 2016 Jun 23.

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

Author information

1
WuXiNextCode Genomics, Sturlugata 8, 101 Reykjavík, Iceland.
2
deCODE Genetics, Sturlugata 8, 101 Reykjavík, Iceland.

Abstract

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 spatial 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/gorpipe CONTACT: hakon@wuxinextcode.comSupplementary information: Supplementary data are available at Bioinformatics online.

PMID:
27339714
PMCID:
PMC5048061
DOI:
10.1093/bioinformatics/btw199
[Indexed for MEDLINE]
Free PMC Article

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