Command line tools

The NCBI Datasets command-line tools (CLI) are datasets and dataformat.

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

Use dataformat to convert metadata from JSON Lines format to other formats.

For more information about our tools, please refer to our How-to guides.

Note: The NCBI Datasets command-line tools are updated frequently to add new features, fix bugs, and enhance usability. Command syntax is subject to change. Please check back often for updates.

Install NCBI Datasets command-line tools

The NCBI Datasets CLI tools are available on multiple platforms.
You can get more information about new features and other updates in our release notes on GitHub.

Install using conda

The NCBI Datasets CLI tools are available as a conda package. It includes both datasets and dataformat.

First, create a conda environment: conda create -n ncbi_datasets

Then, activate your new environment: conda activate ncbi_datasets

Finally, install the datasets conda package: conda install -c conda-forge ncbi-datasets-cli

Install using curl

Linux

Download datasets: curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets'
Download dataformat: curl -o dataformat 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/dataformat'
Make them executable: chmod +x datasets dataformat

macOS

Download datasets: curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/mac/datasets'
Download dataformat: curl -o dataformat 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/mac/dataformat'
Make them executable: chmod +x datasets dataformat

Windows

Download datasets: curl -o datasets.exe "https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/win64/datasets.exe"
Download dataformat: curl -o dataformat.exe "https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/win64/dataformat.exe"