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CGT: COVID-19 Genotyping Tool

Genotyping the viral evolution of SARS-CoV-2 via machine learning


The COVID-19 global pandemic is the greatest healthcare challenge of our time. Whole-genome sequencing (WGS) has provided a means to track SARS-CoV-2 viral genome evolution, which has direct implications for vaccine and therapeutic development. The unprecedented research community effort to make COVID-19 related data accessible has resulted in over 2000 publicly available SARS-CoV-2 WGS sequences on GISAID.

Technology Overview

Researchers at UHN sought to analyze these sequences to gain genomic and epidemiological insights, and deliver them through a web-based R-Shiny application - the COVID-19 Genotyping Tool (CGT).

CGT not only summarizes complex WGS data through informative visualizations such as UMAP and minimum spanning-tree networks, but also allows for users to upload in-house SARS-CoV-2 genome sequencing data for concurrent analysis

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