Before downloading, you must authenticate your session. Run the following command and follow the URL provided to authorize your account: bs auth Use code with caution.
To find the unique ID of the project you want to download, use: bs list projects Use code with caution. download fastq from basespace
The BaseSpace CLI is the most efficient method for downloading entire projects or specific datasets directly to a terminal environment. Before downloading, you must authenticate your session
If you only need data for a specific sample across multiple projects, use the BioSample ID : bs download biosample -i [BiosampleID] -o [DestinationPath] Use code with caution. 2. Download via Web Browser (BaseSpace Downloader) The BaseSpace CLI is the most efficient method
Use the project ID obtained above to download only the compressed FASTQ files:
Downloading FASTQ files from Illumina's BaseSpace Sequence Hub is a common task for bioinformaticians needing to move raw sequencing data to local servers or high-performance computing (HPC) clusters for custom analysis. There are two primary ways to do this: using the for automation or the BaseSpace Downloader for a graphical web interface. 1. Download via BaseSpace CLI (Recommended for Large Data)