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FAQ: How do I download my raw sequencing data?
Christopher Smith avatar
Written by Christopher Smith
Updated over a week ago

You can download raw FastQ files by clicking Download FASTA/Q within the results page for each sample. If you have sequenced your samples with us, or if you have a premium account, the option to download will be displayed below the Compare Sample tile:

Downloading Multiple Samples:

To download multiple samples at once you will need to install the One Codex API - Python Client Library and CLI. This can be done following the instructions here:

The bulk download method described here is using the Command Line Interface (CLI).

Once installed, check your onecodex version. The bulk download of samples is only supported in versions v0.10.0 and above.

onecodex --version 

Next you will need your API Key. This can be found by selecting the account name in the top right corner, then settings. Alternatively using the CLI you login by entering:

onecodex login

This will prompt you to enter your account email and password.

Now you should be ready to download samples using the command:

onecodex --api-key [API_KEY (optional if already logged in)] download samples [Options: --help, --tags TEXT, --project TEXT, --prompt, --no-prompt] [output directory]

An example command downloading all files in the project BATCH1 to the current directory would look like:

onecodex --api-key YOURKEYHERE download samples --project BATCH1 ./

If you are still having trouble downloading your samples, reach out to us by email (, or by clicking on the chat icon at the bottom-right of your screen. We're happy to help!

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