accession
Request genome data by accessions.
datasets download virus genome - download a coronavirus genome dataset by taxon
Download a coronavirus genome dataset including genome, CDS and protein sequence, annotation and a detailed data report. Coronavirus genome datasets are limited to the Coronaviridae family including SARS-CoV-2. Coronavirus genome datasets can be specified by taxon. Datasets are downloaded as a zip file.
The default coronavirus genome dataset includes the following files (if available):
Refer to NCBI’s download and install documentation for information about getting started with the command-line tools.
datasets download virus genome taxon sars-cov-2 --host dog
datasets download virus genome taxon coronaviridae --host "manis javanica"
--annotated limit to annotated coronavirus genomes
--api-key string NCBI Datasets API Key
--complete-only limit to complete coronavirus genomes
--exclude-cds exclude cds.fna (CDS sequence file)
--exclude-protein exclude protein.faa (protein sequence file)
--exclude-seq exclude genomic.fna (genomic sequence file)
--filename string specify a custom file name for the downloaded dataset (default "ncbi_dataset.zip")
--geo-location string limit to coronavirus genomes isolated from a specified geographic location (continent, country or U.S. state)
-h, --help help for genome
--host string limit to coronavirus genomes isolated from a specified host (NCBI Taxonomy ID, scientific or common name at any taxonomic rank)
--lineage string limit to SARS-CoV-2 genomes classified as the specified lineage (variant) by pangolin using the pangoLEARN algorithm
--no-progressbar hide progress bar
--refseq limit to RefSeq coronavirus genomes
--released-since string limit to coronavirus genomes released after a specified date (MM/DD/YYYY)
--updated-since string limit to coronavirus genomes updated after a specified date (MM/DD/YYYY)
Request genome data by accessions.
Request genome data by taxonomic id or name. Allowed taxon are limited to all taxa under Coronaviridae, e.g. sars2 or betacoronavirus