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Total number of samples: 158151

Updated: 2021-06-19 14:12

CRG Viral Beacon - Summary

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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.

Browse dataset through Viral Beacon SARS-CoV-2 Jbrowse instance.

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

Files statistics

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

Number of samples gathered from different resources in Viral Beacon. Some samples may be duplicated or shared across different resources. (Please visit Pipeline page to know about per dataset frequency calculation implemented in Viral Beacon)
Distribution of variant files by sequencing technology by data resource.
Distribution of variant files by collection date by data resource.
Distribution of variant files by host age by data resource.
Distribution of variant files by host sex by data resource.
Distribution of variant files by sample source by data resource.

Variants statistics

Information of variants that were analysed using different data resources.

Distribution of variants by functional class by data resource.
Distribution of variants by mutation type by data resource.
Distribution of variants by genes by data resource.
Distribution of variants by proteins by data resource.

Geographical distribution of SARS-CoV-2 files obtained from different data resources.
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