Options for downloading run folders from BaseSpace Sequence Hub


The Illumina cloud-based genomics computing environment BaseSpace Sequence Hub provides a robust solution for next-generation sequencing data management and analysis. In addition, run data can be downloaded for further analysis using locally installed programs, such as DRAGEN, BCL Convert, bcl2fastq, Local Run Manager, and MiSeq Reporter. While individual files can be downloaded using the BaseSpace Sequence Hub web interface, downloading a full run folder requires tools that communicate directly through the BaseSpace API, using one of the software solutions described in this bulletin.

BaseSpace Command Line Interface (CLI)

Available for Linux, Windows, and Mac OS X, this command line tool can be used to download run data. For downloading runs, you need the run ID number, which is obtained from the URL of the run in BaseSpace or by using the CLI command:

bs list runs

To locate the run ID from a BaseSpace run, refer to the URL, for example:


The digits after “run/” (277282) are the run ID number.

Installation note: The BaseSpace CLI page provides download instructions using either a direct browser download or the wget command.

BaseSpace main CLI

Runs are downloaded with the following command format:

    bs download run -i {RunIDNumber} -o {Destination}

Using the same RunIDNumber and Destination as above, an example command is:

    bs download run -i 277282 -o RunDownload

BaseSpace copy

Note: The separate BaseSpace Copy binary is no longer distributed as the functionality has been incorporated into the main BaseSpace CLI binary as described above. Users with BaseSpace Copy already installed can still download runs with the command format:

    bs-cp -v env:///Run/{RunIDNumber} {Destination}

The default environment value for BaseSpace is https://basespace.illumina.com/. An example command for BaseSpace CLI is:

    bs-cp -v https://basespace.illumina.com/Run/277282 RunDownload


Available for Linux systems, this tool mounts a BaseSpace account as a FUSE filesystem and data is copied via standard command line tools, such as cp and rsync.

Note: The BaseMount installer is currently hosted by bintray, which undergoes periodic maintenance. If you receive a 403 error when trying to download BaseMount, please check the bintray status page for outage reports.