Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes

Summary: We have developed Cake, a bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. Cake can be run on a high-performance computer clus...

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Autores principales: Rashid, Mamunur, Robles-Espinoza, Carla Daniela, Rust, Alistair G., Adams, David J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740632/
https://www.ncbi.nlm.nih.gov/pubmed/23803469
http://dx.doi.org/10.1093/bioinformatics/btt371
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author Rashid, Mamunur
Robles-Espinoza, Carla Daniela
Rust, Alistair G.
Adams, David J.
author_facet Rashid, Mamunur
Robles-Espinoza, Carla Daniela
Rust, Alistair G.
Adams, David J.
author_sort Rashid, Mamunur
collection PubMed
description Summary: We have developed Cake, a bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. Cake can be run on a high-performance computer cluster or used as a stand-alone application. Availabilty: Cake is open-source and is available from http://cakesomatic.sourceforge.net/ Contact: da1@sanger.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-37406322013-08-13 Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes Rashid, Mamunur Robles-Espinoza, Carla Daniela Rust, Alistair G. Adams, David J. Bioinformatics Applications Notes Summary: We have developed Cake, a bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. Cake can be run on a high-performance computer cluster or used as a stand-alone application. Availabilty: Cake is open-source and is available from http://cakesomatic.sourceforge.net/ Contact: da1@sanger.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online. Oxford University Press 2013-09-01 2013-07-16 /pmc/articles/PMC3740632/ /pubmed/23803469 http://dx.doi.org/10.1093/bioinformatics/btt371 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Rashid, Mamunur
Robles-Espinoza, Carla Daniela
Rust, Alistair G.
Adams, David J.
Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes
title Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes
title_full Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes
title_fullStr Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes
title_full_unstemmed Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes
title_short Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes
title_sort cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740632/
https://www.ncbi.nlm.nih.gov/pubmed/23803469
http://dx.doi.org/10.1093/bioinformatics/btt371
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AT rustalistairg cakeabioinformaticspipelinefortheintegratedanalysisofsomaticvariantsincancergenomes
AT adamsdavidj cakeabioinformaticspipelinefortheintegratedanalysisofsomaticvariantsincancergenomes

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