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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...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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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. |
format | Online Article Text |
id | pubmed-5556704 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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