BaseSpace Sequence Hub allows you to download data as a package, individually, or as a group of FASTQ files.

The BaseSpace Sequence Hub Downloader supports downloading files through a proxy server and automatically inherits appropriate settings from the host system. The proxy server must be configured to support the SOCKS4/5 protocol for TCP connections. Contact your network administrator for help with establishing these settings.

Use the BaseSpace Sequence Hub Downloader to download FASTQ or general datasets. Datasets are linked to biosamples and are listed on the Datasets tab of the biosample details page. To download a package of datasets from a run, see Download Run Data Files.

1. From the Biosamples or Projects list, select the biosample or project.

2. Select the FASTQs or Other Datasets tab.

3. [Optional] Select a dataset name to view a list of file details.

4. Select the checkboxes for the desired datasets.

5. Select File, Download, then select Dataset.

6. Select Download. The BaseSpace Sequence Hub Downloader guides you through the download process, and starts the download of the files to the desired location.

Download data from a run as a package of FASTQ files or SAV files. Use the following steps to download a package.

1. Open the desired run.

2. Select File, point to Download, and then select Run.

3. Select the file type you want to download.

• FASTQ—FASTQ files.

• Sequencing Analysis Viewer (SAV)—InterOp and other files required to run SAV.

Data is downloaded in a compressed (*.zip) file format.

Use the BaseSpace Sequence Hub Downloader to download a package of all files in a project.

1. Select Projects.

2. Select a project.

3. Select Download.

The BaseSpace Sequence Hub Downloader guides you through the download process, and starts the download of the files to the desired location.

Use the BaseSpace Sequence Hub Downloader to download whole samples or individual files from a specific sample.

Download Samples

1. From the Projects list, select the project.

2. Select the Samples tab.

3. Select the checkboxes for the desired sample or samples.

4. Select File, Download, then select Sample.

5. Select Download. The BaseSpace Sequence Hub Downloader guides you through the download process, and starts the download of the files to the desired location.

Download Sample Files

1. From the Runs or Projects list, select the run or project.

2. Select the Samples tab.

3. Click the name of the desired sample to access the sample details page.

4. In the Files section, select the checkboxes of the file or files to download.

5. Select "Download Selected". The BaseSpace Sequence Hub Downloader guides you through the download process, and starts the download of the files to the desired location.

If you do not need all of the files in a data set, you can download files individually.

1. Navigate to the analysis file you want to download.

2. Select the file.

3. Select Download.

Use the BaseSpace Sequence Hub Downloader to download a package of analysis files.

1. Select Analyses.

2. Select the checkboxes for the analyses you want to download.

3. Select File, point to Download, then select Analysis.

4. Select the file type you want to download.

• All files including VCF, BAM, & FASTQ

• VCF files only

• BAM files only

1. Select Download. The BaseSpace Sequence Hub Downloader guides you through the download process, and starts the download of the files to the desired location.