CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic
Abstract
Summary
Genome sequences constitute the primary evidence on the origin and spread of the 2019-2020 Covid-19 pandemic. Rapid comparative analysis of coronavirus SARS-CoV-2 genomes is critical for disease control, outbreak forecasting, and developing clinical interventions. CoV Genome Tracker is a web portal dedicated to trace Covid-19 outbreaks in real time using a haplotype network, an accurate and scalable representation of genomic changes in a rapidly evolving population. We resolve the direction of mutations by using a bat-associated genome as outgroup. At a broader evolutionary time scale, a companion browser provides gene-by-gene and codon-by-codon evolutionary rates to facilitate the search for molecular targets of clinical interventions.
Availability and Implementation
CoV Genome Tracker is publicly available at<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://cov.genometracker.org">http://cov.genometracker.org</ext-link>and updated weekly with the data downloaded from GISAID (<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://gisaid.org">http://gisaid.org</ext-link>). The website is implemented with a custom JavaScript script based on jQuery (<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://jquery.com">https://jquery.com</ext-link>) and D3-force (<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/d3/d3-force">https://github.com/d3/d3-force</ext-link>).
Contact
<email>weigang@genectr.hunter.cuny.edu</email>, City University of New York, Hunter College
Supplementary Information
All supporting scripts developed in JavaScript, Python, BASH, and PERL programming languages are available as Open Source at the GitHub repository<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/weigangq/cov-browser">https://github.com/weigangq/cov-browser</ext-link>.
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