Speaker
Description
Interactive web dashboards have proven to be effective tools for exploring and communicating epidemiological insights obtained from genomic data. In particular, they are valuable for large and/or regularly updated datasets, facilitating real-time monitoring and the rapid identification of new variants and transmission patterns. During the SARS-CoV-2 pandemic, many new genomic epidemiological dashboards were developed; however, similar resources for other pathogens remain scarce, and no reusable software has been available to simplify the creation of dashboards for emerging diseases.
The GenSpectrum project aims to close this gap. Building on experiences from the CoV-Spectrum dashboard, we offer three tools:
- A public dashboard (available at genspectrum.org), which leverages open data from INSDC and Pathoplexus, supports multiple pathogens, including influenza, RSV, SARS-CoV-2, Ebola virus, West Nile virus, and mpox virus – with more pathogens to be added in the near future. This dashboard provides various views, enabling users to filter variants by lineage or mutation profile, explore spatiotemporal distributions, analyze mutations, assess growth advantage, review sequencing technologies, and more.
- A Web Components library, offering individual plots and search widgets that can be integrated into other websites and build new dashboards.
- A database query engine (LAPIS/SILO), written in C++ and Kotlin, designed for high efficiency. This engine supports specialized genomic operations which are not available in general-purpose databases such as mutation and sub-lineage queries and calculations of mutation distributions – typically within 100ms for millions of sequences.
All tools are open source. In our presentation, we explain the core algorithms and concepts of the framework and present use cases for the tools.
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