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

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 archi...

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Autores principales: Guðbjartsson, Hákon, Georgsson, Guðmundur Fr., Guðjónsson, Sigurjón A., Valdimarsson, Ragnar þór, Sigurðsson, Jóhann H., Stefánsson, Sigmar K., Másson, Gísli, Magnússon, Gísli, Pálmason, Vilmundur, Stefánsson, Kári
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5048061/
https://www.ncbi.nlm.nih.gov/pubmed/27339714
http://dx.doi.org/10.1093/bioinformatics/btw199
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author Guðbjartsson, Hákon
Georgsson, Guðmundur Fr.
Guðjónsson, Sigurjón A.
Valdimarsson, Ragnar þór
Sigurðsson, Jóhann H.
Stefánsson, Sigmar K.
Másson, Gísli
Magnússon, Gísli
Pálmason, Vilmundur
Stefánsson, Kári
author_facet Guðbjartsson, Hákon
Georgsson, Guðmundur Fr.
Guðjónsson, Sigurjón A.
Valdimarsson, Ragnar þór
Sigurðsson, Jóhann H.
Stefánsson, Sigmar K.
Másson, Gísli
Magnússon, Gísli
Pálmason, Vilmundur
Stefánsson, Kári
author_sort Guðbjartsson, Hákon
collection PubMed
description 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.com Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-50480612016-10-05 GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture Guðbjartsson, Hákon Georgsson, Guðmundur Fr. Guðjónsson, Sigurjón A. Valdimarsson, Ragnar þór Sigurðsson, Jóhann H. Stefánsson, Sigmar K. Másson, Gísli Magnússon, Gísli Pálmason, Vilmundur Stefánsson, Kári Bioinformatics Original Paper 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.com Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2016-10-15 2016-06-23 /pmc/articles/PMC5048061/ /pubmed/27339714 http://dx.doi.org/10.1093/bioinformatics/btw199 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Original Paper
Guðbjartsson, Hákon
Georgsson, Guðmundur Fr.
Guðjónsson, Sigurjón A.
Valdimarsson, Ragnar þór
Sigurðsson, Jóhann H.
Stefánsson, Sigmar K.
Másson, Gísli
Magnússon, Gísli
Pálmason, Vilmundur
Stefánsson, Kári
GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture
title GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture
title_full GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture
title_fullStr GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture
title_full_unstemmed GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture
title_short GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture
title_sort gorpipe: a query tool for working with sequence data based on a genomic ordered relational (gor) architecture
topic Original Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5048061/
https://www.ncbi.nlm.nih.gov/pubmed/27339714
http://dx.doi.org/10.1093/bioinformatics/btw199
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