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GeMSTONE: orchestrated prioritization of human germline mutations in the cloud.


ABSTRACT: 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.

SUBMITTER: Chen S 

PROVIDER: S-EPMC5556704 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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GeMSTONE: orchestrated prioritization of human germline mutations in the cloud.

Chen Siwei S   Beltrán Juan F JF   Esteban-Jurado Clara C   Franch-Expósito Sebastià S   Castellví-Bel Sergi S   Lipkin Steven S   Wei Xiaomu X   Yu Haiyuan H  

Nucleic acids research 20170701 W1


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 wi  ...[more]

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