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Illumina BaseSpace


llumina BaseSpace command line client,bs, can be used to retrievie data from the Illumina BaseSpace environment to Puhti.


Software is free to use.


  • Puhti: 1.0.0


First load the biokit module

module load biokit

When biokit is loaded, the Illumina BaseSpace command line client starts with command:


To be able to use this service you must have an account in the Illumina Base Space service.

As the first step you must set up your authentication so that you can access your data in Illumina BaseSpace. This is done by running command:

bs auth

The authentication information is stored to your home directory in Puhti ($HOME/.basespace/default.cfg). Thus the authentication needs to be done only once.

After that you can start working with your Illumina data. For example, available datasets can be listed with command:

bs list datasets

Single dataset can be downloaded to Puhtri with command:

bs download dataset -i dataset_id -o local_download_dir


More detailed information about using Illumne BaseSpace client can be found form the links below :

Last update: October 10, 2022