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COVID-19 Viral Genome Analysis Pipeline
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External Tools

Tools, Software, and Information for SARS-CoV-2


Coronavirus Genetic Analysis and Variants

The GISAID initiative promotes the rapid sharing of data from all influenza viruses and the SARS-CoV-2 coronavirus causing COVID-19. This includes genetic sequence and related clinical and epidemiological data associated with human viruses, and geographical as well as species-specific data associated with avian and other animal viruses, to help researchers understand how viruses evolve and spread during epidemics and pandemics.

Pangolin ( assigns and names the variant lineages of SARS-CoV-2. The Pango nomenclature is being used by researchers and public health agencies worldwide to track the transmission and spread of SARS-CoV-2, including variants of concern.

COVID CG provides global lineage surveillance tools.

CDC Variants information Information about the characteristics of these variants is rapidly emerging. Scientists are working to learn more about how easily they spread, whether they could cause more severe illness, and whether currently authorized vaccines will protect people against them.

WHO: Tracking SARS-CoV-2 variants The World Health Organization provide information about SARS-CoV-2 variants, working definitions and actions taken.

NextStrain Genomic epidemiology of novel coronavirus - Global subsampling, illustrates the phylogeny of a downsampled subset of genomes in the GISAID database.

Edge Bioinformatics provides automated genome assembly and helps users create a good file for CoV Genbank submission.

Edge Bioinformatics Assay Validation provides in silico evaluation of diagnostic assays.

Pangolin SARS-CoV-2 genotyping tool performs genotyping of SARS-Cov-2 sequences.

The A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology Nomenclature for SARS-CoV-2 genotypes. Andrew Rambaut, Edward C. Holmes, Verity Hill, Áine O’Toole, JT McCrone, Chris Ruis, Louis du Plessis, Oliver G. Pybus. “A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology”. bioRxiv 2020.04.17.046086; doi:

The Coronavirus Genotyping Tool uses phylogenetic methods to identify cornoavirus genotype. A paper describing the tool has been published.

The Year-letter Genetic Clade Naming for SARS-CoV-2 on describes the clades and names proposed by

Natural selection analysis of global SARS-CoV-2/COVID-19

Coronavirus Reference Strain Sequences

NC_045512 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome.

NC_004718 SARS coronavirus Tor2 genome, reference genome for SARS coronavirus.

NC_019843 Middle East respiratory syndrome coronavirus, complete genome. Reference genome for MERS coronavirus.

COVID-19 Epidemiology is a project from Scripps Research to unify COVID-19 and SARS-CoV-2 epidemiology and genomic data, published research, and other resources. Researchers, health officials, and the public can track the pandemic using data on cases, deaths, and genomic variants, and stay updated on related research through interactive visualizations, a searchable library, and downloadable raw data.

An interactive visualization of the exponential spread of COVID-19, a web based tool for visualizing COVID-19 case data over time by geographic region.

NCBI SARS-2 COVID-19 data entry page for SARS-Cov-2 genomic data and PubMed searching on papers related to the COVID-19 pandemic.

An interactive visualization of the exponential spread of COVID-19 at the National Institutes of Health (NIH), maintained by the National Institute of Allergy and Infectious Diseases (NIAID)

Other SARS-Cov-2 and COVID-19 Tools and Research Resources

World Health Organization COVID-19 Information

World Health Organization COVID-19 Situation Reports

USA Centers for Disease Control COVID-19 Information.

CoronaWhy is a globally distributed, volunteer-powered research organisation, trying to assist the medical community's ability to answer key questions related to COVID-19

COVID-19 Data Portal The European Commission and EMBL’s European Bioinformatics Institute (EMBL-EBI), together with EU Member States and research partners such as ELIXIR, operate a dedicated European COVID-19 Data Platform that enables the rapid collection and comprehensive data sharing of available research data from different sources for the European and global research communities. It includes host genes/proteins of interest to COVID-19 research.

SARS-CoV-2 Vaccine Trials Information

COVID-19 vaccine tracker This tracker lists COVID-19 vaccine candidates currently in Phase 1-3 trials, as well as major candidates in pre-clinical stages of development and research. Information will be updated weekly.

COVID-19 Clinical Trials An online, open access database set up by the Anticancer Fund (ACF, Brussels, Belgium) gives details of over 200 clinical trials for COVID-19 therapeutic techniques. The database currently contains 263 clinical trials taking place worldwide and gives insight into the type of drug candidates being tested.

COVID-19 Confirmed and Forecasted Case Data Current cases and forecast

CDC Case count by USA county.

Johns Hopkins -compiled USA county-level case counts, and global case counts information.

New York Times-compiled USA county-level case counts (numerical data).

US data including testing rates and results, hospitalization data, and data quality scores (The Atlantic).

Interactive worldwide infection data.

Financial Times (London) worldwide fixed and interactive plots, including historical death rate comparisons.

The US Covid Atlas (UChicago).


last modified: Wed Aug 25 11:52 2021

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