Logo for CRG Viral Beacon

Total number of samples: 71365

Updated: 2020-05-12 00:00

CRG Viral Beacon - Summary

CRG Covid Viral Beacon is a tool to find SARS-CoV-2 variability at genomic, amino acid and motif level. It offers the possibility to (i) search in detail about the genomic variants, (ii) filter queries and find unique cases, (iii) filter strain/country-specific variants, (iv) explore associated metadata and much more.

CRG Covid Viral Beacon is a tool for those interested in the SARS-CoV-2 variability, mainly at genomic scale, but also related changes such as at aminoacid level along with other metadata. It has been developed as a branch of the GA4GH Beacon standard, as a special use case for testing and demonstration of new features in Beacon v2 (and implicitly of Beacon v1). As a use case, SARS-CoV-2 gave us the opportunity to work on a small genome but its importance and urgency catalysed us to help focus on the utility of the features. It is well suited for all the features that Beacon v2 currently have: diversity of queries, filters, additional schemas for core entities, handover to other solutions or extended data, etc. It has been organised as an iterative project, starting with a quick solution for determining requirements and usage and gradually shifting to an orthodox Beacon v2 API interface, e.g. at the first iteration data is presented "as is", without any harmonisation nor pre-processing from our side. Although driven by the EGA Team at CRG, it should be considered a joint effort between our institution, our partners and our founders.


Distribution of variants (frequency >= 0.005) of SARS-CoV-2 genome obtained from different data resources.
Geographical distribution of SARS-CoV-2 files obtained from different data resources.

File statistics

Information of data resources that have been utilized in Covid Viral Beacon.

Distribution of variant files by data resource.
Distribution of variants by sequencing technology by data resource.
Distribution of variants by collection date by data resource.
Distribution of variants by host age by data resource.
Distribution of variants by host sex by data resource.
Distribution of variants by sample source by data resource.

Variant statistics

Information of variants that were analysed using different data resources.

Distribution of variant by functional class by data resource.