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 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)

BaseSpace Command Line Interface (CLI) is available for Linux, Windows (32 and 64 bit), and Mac OS X, this command line tool is used to download run data using either the BaseSpace copy (bs-cp) or main CLI (bs) programs. For some run folders, in particular run folders containing thumbnail images, the BaseSpace copy program may download the run faster than the main CLI program because it handles large numbers of small files more efficiently. For both programs, 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 the wget command. If wget is not available on your system, the direct download links within the download commands are used instead.

BaseSpace copy

Runs are downloaded 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

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


BaseMount is 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.