accession
Download a virus genome data package by accession.
accession
Name
datasets download virus genome accession - Download a virus genome data package by accession.
Synopsis
datasets download virus genome accession <accession ...> [flags]
Description
Download a virus genome data package by GenBank or RefSeq nucleotide accession. Virus genome data packages include genome, transcript and protein sequences, annotation and one or more data reports. Data packages are downloaded as a zip archive.
The default virus genome data package includes the following files:
- genomic.fna (genomic sequences)
- data_report.jsonl (data report with virus genome metadata)
- dataset_catalog.json (a list of files and file types included in the data package)
Examples
datasets download virus genome accession NC_045512.2 --include genome,cds,protein
Options
--annotated Limit to annotated genomes
--api-key string Specify an NCBI API key
--complete-only Limit to complete genomes
--debug Emit debugging info
--filename string Specify a custom file name for the downloaded data package (default "ncbi_dataset.zip")
--geo-location string Limit to genomes isolated from a specified geographic location (continent, country or U.S. state)
--help Print detailed help about a datasets command
--host string Limit to virus genomes isolated from a specified host species
--include string(,string) Specify virus genome sequence types to download
* genome: genomic sequences
* cds: nucleotide coding sequences
* protein: amino acid sequences
* annotation: annotation report
* biosample: biosample report
* none: no sequence data, only primary data report
(default [genome])
--inputfile string Read a list of nucleotide accessions from a file to use as input
--lineage string Limit results by Pango lineage (only SARS-CoV-2)
--no-progressbar Hide progress bar
--released-after string Limit to genomes released on or after a specified date (MM/DD/YYYY)
--updated-after string Limit to genomes updated on or after a specified date (MM/DD/YYYY)
--version Print version of datasets
Generated April 19, 2024