RT Journal Article
SR Electronic
T1 CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.04.10.036343
DO 10.1101/2020.04.10.036343
A1 Saymon Akther
A1 Edgaras Bezrucenkovas
A1 Brian Sulkow
A1 Christopher Panlasigui
A1 Li Li
A1 Weigang Qiu
A1 Lia Di
YR 2020
UL http://biorxiv.org/content/early/2020/04/14/2020.04.10.036343.abstract
AB 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 http://cov.genometracker.org and updated weekly with the data downloaded from GISAID (http://gisaid.org). The website is implemented with a custom JavaScript script based on jQuery (https://jquery.com) and D3-force (https://github.com/d3/d3-force).Contact weigang{at}genectr.hunter.cuny.edu, City University of New York, Hunter CollegeSupplementary Information All supporting scripts developed in JavaScript, Python, BASH, and PERL programming languages are available as Open Source at the GitHub repository https://github.com/weigangq/cov-browser.Competing Interest StatementThe authors have declared no competing interest.