Beacon v2 Reference Implementation

To demonstrate Beacon v2 capabilities and to facilitate the adoption, ELIXIR organization has been funding the development of the Beacon v2 Reference Implementation (B2RI). Developed at the Centre for Genomic Regulation (CRG), the B2RI is a free open source Linux-based set of tools that allow lighting up a Beacon out-of-the-box.

The B2RI includes:

  1. Tools for loading metadata (including phenotypic data) and genomic variants (from a VCF file) into a database.
  2. A MongoDB database.
  3. The Beacon query engine (i.e., REST API).
  4. An example dataset consisting of synthetic-data (CINECA synthetic cohort EUROPE UK1).

The B2RI is conceived as a customizable local solution, delivered with a basic configuration. The software is written in Python, Perl and Bash and has a command-line interface (CLI) for control and operation.


Rueda, M, Ariosa R. "Beacon v2 Reference Implementation: a toolkit to enable federated sharing of genomic and phenotypic data". Bioinformatics, btac568, DOI.


This study was funded by ELIXIR, the research infrastructure for life-science data (ELIXIR Beacon Implementation Studies 2019-2021 and 2022-2023).