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precisionFDA is a cloud based platform that provides an environment where the community can test, pilot, and benchmark new approaches to validating their next-generation sequencing (NGS) analysis pipelines. PrecisionFDA offers community members a secure and independent work area where, at their discretion, their bioinformatics tools or data can …

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README.md

PrecisionFDA

PrecisionFDA is a community platform for NGS assay evaluation and regulatory science exploration, accessible at https://precision.fda.gov/

Webapp

The code in this repository represents the precisionFDA webapp, which uses the Ruby on Rails framework. For more information on that framework, visit:

http://guides.rubyonrails.org/

Installation of ruby dependencies is handled via bundler, and asset management is done via bower.

Operation of the webapp relies on an upstream cloud backend, for services such as user authentication, file storage and VM execution. The site deployed at https://precision.fda.gov/ uses DNAnexus as the cloud provider.

PrecisionFDA command-line uploader

In addition to the webapp, this repo hosts the precisionFDA command-line uploader. It can be found under the tools folder.

Apps and other content

The deployed precisionFDA site includes content such as app assets, apps, reference data, etc. Such content is added on top of the website and is not part of this repository. You can access such public contributions on https://precision.fda.gov/ where you can download files and app assets, as well as fork apps to access their scripts.

Comparison framework

The current comparison app runs vcfeval from Real Time Genomics. You can access it at the following GitHub repo:

https://github.com/RealTimeGenomics/rtg-tools

Development setup

To set up development environment please refer to Development Setup.

React-based frontend development

To get information about React-based development, please refer to this manual.

About

precisionFDA is a cloud based platform that provides an environment where the community can test, pilot, and benchmark new approaches to validating their next-generation sequencing (NGS) analysis pipelines. PrecisionFDA offers community members a secure and independent work area where, at their discretion, their bioinformatics tools or data can …

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