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NCBI Datasets is a resource that lets you easily gather data from across NCBI databases. You can use it to find and download sequence, annotation, and metadata for genes and genomes using our command-line interface (CLI) tools orNCBI Datasets web interface.

NCBI Datasets tools are under active development. To submit feedback, please create aGitHub issue orcontact NCBI directly with your questions, comments or feature requests.

Install the latest version (CLI v16.x) of the NCBI Datasets CLI tools,datasets anddataformat, using conda:

conda install -c conda-forge ncbi-datasets-cli

For other installation options, see our CLI toolsdownload and install instructions.

Usedatasets to download biological sequence data across all domains of life from NCBI.

Usedataformat to convert metadata included as part of the data package from JSON Lines format to other formats.

Usedatasets to download a genome data package for the human reference genome GRCh38:

datasets download genome taxon human --reference --filename human-reference.zip

Usedataformat to extract selected fields of metadata from the downloaded data package for the human reference genome, GRCh38:

dataformat tsv genome --package human-reference.zip --fields organism-name,assminfo-name,accession,assminfo-submitterOrganism nameAssembly NameAssembly AccessionAssembly SubmitterHomo sapiensGRCh38.p14GCF_000001405.40Genome Reference Consortium

The Datasets CLI schematic below also outlines the available commands for thedatasets CLI.

Download large numbers of genomes by first downloading a dehydrated zip archive and then accessing the data in three steps.

1. Download the dehydrated zip archive
2. Unzip the downloaded zip archive
3. Rehydrate to access the data

Try this example for the human reference genome:

1. Download the dehydrated zip archive:
   datasets download genome accession GCF_000001405.40 --dehydrated --filename human_GRCh38_dataset.zip

2. Unzip the downloaded zip archive:
   unzip human_GRCh38_dataset.zip -d my_human_dataset

3. Rehydrate to access the data:
   datasets rehydrate --directory my_human_dataset/

For more information, seehow to download large genome data packages.

NCBI Datasets API and command-line tool requests are rate-limited. By default, this rate limit is set at 5 requests per second (rps). By using your API key, you can increase this rate limit to 10 rps. For more information, see our documentation onhow to get an API key andhow to use your API key.

NCBI Datasets provides sequence, annotation, metadata and other biological data asNCBI Datasets Data Package zip archives.

We currently offer four types of data package:

1. AnNCBI Datasets Gene Data Package
2. AnNCBI Datasets Genome Data Package
3. A specializedNCBI Datasets Virus Data Package.
4. AnNCBI Datasets Taxonomy Data Package

NCBI Datasets data packages include data report files that contain metadata about the requested records.Data report schemas describe each type of data report, including available fields, with descriptions and examples.

O'Leary NA, Cox E, Holmes JB, Anderson WR, Falk R, Hem V, Tsuchiya MTN, Schuler GD, Zhang X, Torcivia J, Ketter A, Breen L, Cothran J, Bajwa H, Tinne J, Meric PA, Hlavina W, Schneider VA.Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets. Sci Data. 2024 Jul 5;11(1):732. doi: 10.1038/s41597-024-03571-y. PMID: 38969627; PMCID: PMC11226681.