This is a list of links to websites and software that can be used for SARS-CoV-2 sequence analysis and epidemiology of strains / mutations.
Not included are dashboards that show general SARS-CoV-2 statistics, e.g., the number of cases per region, etc.
- About the PANGO nomenclature
- Pangolin web server for assigning PANGO lineages to assembled genomes
- Nextclade, clade assignment, mutation calling, and sequence quality checks
- Nextstrain
- UShER, place sequences in a global phylogenetic tree
- Gensplore MN908947, browse the reference genome
- Codon2Nucelotide, convert from codon position to genomic coordinates or vice versa
- Cov2Tree
- Outbreak.info
- CoVizu
- CoV-Spectrum, easy queries for filtering by strains and/or mutations
- CoVariants
- COVID-19 virus mutation tracker
- COG-UK Mutation Explorer
- Pangolin, also via bioconda
- Nextclade CLI, also via bioconda
- connor-lab/ncov2019-artic-nf, nextflow-based pipeline for generating consensus sequences from amplicon-sequencing
- CoronaCentral.ai, literature search for SARS-CoV-2 and other viruses