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GeMSTONE: orchestrated prioritization of human germline mutations in the cloud

Integrative analysis of whole-genome/exome-sequencing data has been challenging, especially for the non-programming research community, as it requires simultaneously managing a large number of computational tools. Even computational biologists find it unexpectedly difficult to reproduce results from...

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Autores principales: Chen, Siwei, Beltrán, Juan F., Esteban-Jurado, Clara, Franch-Expósito, Sebastià, Castellví-Bel, Sergi, Lipkin, Steven, Wei, Xiaomu, Yu, Haiyuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5556704/
https://www.ncbi.nlm.nih.gov/pubmed/28521008
http://dx.doi.org/10.1093/nar/gkx398
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author Chen, Siwei
Beltrán, Juan F.
Esteban-Jurado, Clara
Franch-Expósito, Sebastià
Castellví-Bel, Sergi
Lipkin, Steven
Wei, Xiaomu
Yu, Haiyuan
author_facet Chen, Siwei
Beltrán, Juan F.
Esteban-Jurado, Clara
Franch-Expósito, Sebastià
Castellví-Bel, Sergi
Lipkin, Steven
Wei, Xiaomu
Yu, Haiyuan
author_sort Chen, Siwei
collection PubMed
description Integrative analysis of whole-genome/exome-sequencing data has been challenging, especially for the non-programming research community, as it requires simultaneously managing a large number of computational tools. Even computational biologists find it unexpectedly difficult to reproduce results from others or optimize their strategies in an end-to-end workflow. We introduce Germline Mutation Scoring Tool fOr Next-generation sEquencing data (GeMSTONE), a cloud-based variant prioritization tool with high-level customization and a comprehensive collection of bioinformatics tools and data libraries (http://gemstone.yulab.org/). GeMSTONE generates and readily accepts a shareable ‘recipe’ file for each run to either replicate previous results or analyze new data with identical parameters and provides a centralized workflow for prioritizing germline mutations in human disease within a streamlined workflow rather than a pool of program executions.
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spelling pubmed-55567042017-08-28 GeMSTONE: orchestrated prioritization of human germline mutations in the cloud Chen, Siwei Beltrán, Juan F. Esteban-Jurado, Clara Franch-Expósito, Sebastià Castellví-Bel, Sergi Lipkin, Steven Wei, Xiaomu Yu, Haiyuan Nucleic Acids Res Web Server Issue Integrative analysis of whole-genome/exome-sequencing data has been challenging, especially for the non-programming research community, as it requires simultaneously managing a large number of computational tools. Even computational biologists find it unexpectedly difficult to reproduce results from others or optimize their strategies in an end-to-end workflow. We introduce Germline Mutation Scoring Tool fOr Next-generation sEquencing data (GeMSTONE), a cloud-based variant prioritization tool with high-level customization and a comprehensive collection of bioinformatics tools and data libraries (http://gemstone.yulab.org/). GeMSTONE generates and readily accepts a shareable ‘recipe’ file for each run to either replicate previous results or analyze new data with identical parameters and provides a centralized workflow for prioritizing germline mutations in human disease within a streamlined workflow rather than a pool of program executions. Oxford University Press 2017-07-03 2017-05-18 /pmc/articles/PMC5556704/ /pubmed/28521008 http://dx.doi.org/10.1093/nar/gkx398 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution 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 Web Server Issue
Chen, Siwei
Beltrán, Juan F.
Esteban-Jurado, Clara
Franch-Expósito, Sebastià
Castellví-Bel, Sergi
Lipkin, Steven
Wei, Xiaomu
Yu, Haiyuan
GeMSTONE: orchestrated prioritization of human germline mutations in the cloud
title GeMSTONE: orchestrated prioritization of human germline mutations in the cloud
title_full GeMSTONE: orchestrated prioritization of human germline mutations in the cloud
title_fullStr GeMSTONE: orchestrated prioritization of human germline mutations in the cloud
title_full_unstemmed GeMSTONE: orchestrated prioritization of human germline mutations in the cloud
title_short GeMSTONE: orchestrated prioritization of human germline mutations in the cloud
title_sort gemstone: orchestrated prioritization of human germline mutations in the cloud
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5556704/
https://www.ncbi.nlm.nih.gov/pubmed/28521008
http://dx.doi.org/10.1093/nar/gkx398
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