Skip to content

Downloading NGS Data with Cyberduck

Cyberduck is a free and open-source SFTP client that allows you to easily download NGS (Next-Generation Sequencing) data from the XLence cluster to your local computer using a simple drag-and-drop interface.

Network Access Requirements

Important: Access to NGS data is available when you are connected to the university network.

About Cyberduck

Cyberduck can be used free of charge without registration. The software is donation-based and may occasionally prompt you to donate, but you can continue using it for free by clicking "Later" or closing the donation dialog.

Download and Installation

macOS

Cyberduck is available as a universal binary that runs natively on both Intel and Apple Silicon (M1/M2/M3) Macs.

Download: 1. Visit https://cyberduck.io/download/ 2. Click "Download Cyberduck for Mac" 3. Open the downloaded .zip file 4. Drag the Cyberduck app to your Applications folder

Requirements: macOS 10.13 or later

Windows

Download: 1. Visit https://cyberduck.io/download/ 2. Click "Download Cyberduck for Windows" 3. Run the downloaded installer (.exe file) 4. Follow the installation wizard

Requirements: Windows 10 or later

Configuration

Create a Bookmark for NGS Data Access

To easily access NGS data, create a bookmark with the following settings:

  1. Open Cyberduck and click the "+" button (bottom left) to create a new bookmark

  2. Configure the bookmark with these settings:

  3. Protocol: SFTP (SSH File Transfer Protocol)

  4. Nickname: NGS-DATA (or any name you prefer)
  5. Server: xlence.disfeb.unimi.it
  6. Port: 22
  7. Username: Your cluster username (e.g., uliano.guerrini)
  8. Password: Your cluster password (optional - you can enter it each time)

  9. SSH Private Key: None (unless you use SSH keys)

  10. Expand "More Options" and set:

  11. Path: /data/ngs/Illumina (this is the directory containing NGS datasets)

  12. Close the bookmark dialog - the bookmark is saved automatically

Cyberduck Bookmark Configuration

Note: The configuration shows the path to the Illumina NGS data folder. If you need to access different data types or directories, modify the Path field accordingly.

Connecting and Downloading Data

Connect to the Cluster

  1. Double-click the bookmark you just created
  2. If you didn't save your password, enter it when prompted
  3. You may see a security warning about the SSH host key - click "Allow" or "Always" to continue

Browse and Download NGS Datasets

Once connected, you'll see a list of NGS datasets organized in folders.

NGS Data Folder Example

Dataset Organization: - Each dataset is stored in a folder with the acquisition date included in the folder name - Folder names follow the format: YYMMDD_[run_info] (e.g., 251006_NB552283_0069_AHKWG5BGXW was acquired on October 6, 2025) - Datasets are sorted by date with the most recent at the top

Download Datasets

To download a dataset to your computer:

  1. Locate the dataset you want to download (check the date in the folder name)
  2. Drag and drop the folder from Cyberduck to any location on your computer (Desktop, Documents, etc.)
  3. Cyberduck will begin the download - a progress indicator will show the transfer status
  4. Large datasets may take time to download depending on your network connection

Tips: - You can download multiple folders at once by selecting them (Cmd+Click on Mac, Ctrl+Click on Windows) - Right-click any folder and select "Download" to choose a specific destination - Downloads resume automatically if interrupted

Troubleshooting

Connection Issues

  • Cannot connect from home: Make sure you have an active VPN connection to the university network
  • Authentication failed: Verify your username and password are correct (same credentials used for SSH access)
  • Host key warning: This is normal on first connection - click "Allow" to proceed

Download Issues

  • Slow transfers: Large NGS datasets can be several gigabytes - ensure you have a stable network connection
  • Insufficient disk space: Check that you have enough free space on your computer before downloading large datasets
  • Transfer interrupted: Cyberduck will automatically resume downloads if the connection is lost

Alternative Methods

If you prefer command-line tools or need to automate downloads, you can also use:

  • SFTP command line: sftp username@xlence.disfeb.unimi.it
  • SCP command: scp -r username@xlence.disfeb.unimi.it:/data/ngs/Illumina/dataset_folder ./local_destination
  • rsync: For incremental/resumable transfers

For more information on SFTP clients, see the SFTP File Transfer Clients guide.