Resources
A curated list of tools, software, dashboards, and data sources for analyzing and visualizing SARS-CoV-2 data.
Internally Developed Tools
Pangolin
Assigns Pango lineages to SARS-CoV-2 genome sequences.
Scorpio
A tool for SNP-based calling of variants of concern.
Civet
Generates reports for outbreak investigations.
Polecat
Identifies and flags clusters based on configurable statistics.
Dashboards
Outbreak.info
Dashboard for viewing information about SARS-CoV-2 variants.
CoVariants
Overview of SARS-CoV-2 variants and interesting mutations.
covSPECTRUM
Interactive dashboard for SARS-CoV-2 variants with sophisticated queries.
JHU Covid-19 Dashboard
Dashboard displaying information about the general spread of Covid-19.
Lineage Tree
Interactive visualisation of the Pango lineage system.
COG Mutation Explorer
Data visualisation tool for exploring SARS-CoV-2 variants and mutations.
Software Tools
CoViT
Enables real-time phylogenetics for the SARS-CoV-2 pandemic using Vision Transformers.
PanGUIlin
A web application version of the Pangolin Tool.
Nextstrain
Powerful, interactive tools for exploring virus data.
UShER Phylogenetic Placement
Finds the most similar samples from public sequence databases.
Data Sources
GISAID
Global data repository for SARS-CoV-2 genomes.
European Nucleotide Archive (ENA)
High quality, downloadable data set of SARS-CoV-2 genomes.
COG-UK
Large number of data sets and bioinformatics tools for SARS-CoV-2.