Resources

Internally Developed Tools

software

Pangolin

Pangolin was developed to implement the dynamic nomenclature of SARS-CoV-2 lineages, known as the Pango nomenclature. It allows a user to assign a SARS-CoV-2 genome sequence the most likely lineage (Pango lineage) to SARS-CoV-2 query sequences.

Pangolin assigns lineages to query sequences as described in Rambaut et al 2020.



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software

Scorpio

Serious constellations of reoccurring phylogenetically-independent origin. A tool for snp-based calling of variants of concern.



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software

Pando

View and interact with the latest global SARS-COV-2 phylogenic tree



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software

Civet

Civet is a tool developed with 'real-time' genomics in mind.

Using a background phylogeny, such as the large phylogeny available through the COG-UK infrastructure on CLIMB, civet will generate a report for a set of sequences of interest i.e. an outbreak investigation.



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software

Polecat

Using a background phylogeny, such as the large phylogeny available through the COG-UK infrastructure on CLIMB, polecat will identify and flag clusters based on various configurable statistics.



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website

pango.network

A website documenting the Pango nomenclature as well as the policies involved with designating new lineages.



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Dashboards

Su, Wu, and Andersen labs at Scripps Research

Outbreak.info

A data dashboard for viewing more information about the various SARS-COV-2 variants



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Emma Hodcroft, University of Bern, Switzerland

CoVariants

A dashboard giving an overview of SARS-CoV-2 variants and interesting mutations



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Computational Evolution group at ETH Zurich, Switzerland

covSPECTRUM

An interactive dashboard SARS-CoV-2 variants with sophisticated queries



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Center for Systems Science and Engineering at Johns Hopkins University

JHU Covid-19 Dashboard

An interactive dashboard displaying various information about the general spread of Covid-19.



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COG-UK

COG Mutation Explorer

A data visualisation tool for exploring important SARS-CoV-2 variants and mutations



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Software Tools

Centre for Genomic Pathogen Surveillance

PanGUIlin

A web application version of the Pangolin Tool



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Trevor Bedford et al

Nextstrain

Powerful, interactive tools for exploring virus data. Nextstrain provides a large database of viral genomes and bioinformatics pipelines for phylogenetic analysis, including interactive tree visualisations.



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Angie Hinrichs, UC Santa Cruz Genomics Institute

UShER Phylogenetic Placement

Upload your SARS-CoV-2 sequence (FASTA or VCF file) to find the most similar complete, high-coverage samples from GISAID or from public sequence databases (NCBI Virus / GenBank, COG-UK and the China National Center for Bioinformation), and your sequence's placement in the phylogenetic tree generated by the sarscov2phylo pipeline.



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Data Sources

GISAID

GISAID

Important, global data repository for SARS-COV-2 genomes as well as for other pathogens



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ENA

European Nucleotide Archive

The ENA provides a high quality, downloadable data set of SARS-CoV-2 genomes. ENA data is available as a data source on Galaxy.



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COG-UK

COG-UK

COG-UK provides a large number of data sets and bioinformatics tools for SARS-COV-2.



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