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How to Retrieve NGS Data

This page explains how to access and download NGS sequencing data from the XLence cluster.

⚠️ Important Notice

The cluster is NOT a backup service. NGS data stored on XLence is temporary storage only.

You are responsible for: - Downloading your sequencing data promptly - Backing up data to your own storage systems - Understanding that data may be removed after a reasonable time period

Prerequisites

Before retrieving NGS data, ensure you have completed the Access Prerequisites section in the "How to Get Access" page. You need:

  • Valid INDACO registration
  • Cluster account activation
  • SSH access configured

Easy Way: Download with Cyberduck

The easiest method to download NGS data is using Cyberduck, a free graphical SFTP client with drag-and-drop functionality.

👉 Download with Cyberduck - Complete step-by-step guide including: - Installation for macOS and Windows - Bookmark configuration - Drag-and-drop file transfer - VPN access requirements

Data Location

[To be completed with specific paths and instructions]

NGS sequencing runs are typically stored in:

/path/to/ngs/data/

Accessing Your Data

1. Via SSH and SCP

[To be completed with detailed instructions]

# Connect to the cluster
ssh username@xlence.disfeb.unimi.it

# Navigate to your data directory
cd /path/to/your/data

# Check data size
du -sh .

# Download to your local machine (from your local terminal)
scp -r username@xlence.disfeb.unimi.it:/path/to/data /local/destination/

[To be completed with rsync instructions]

# Sync data from cluster to local
rsync -avz --progress username@xlence.disfeb.unimi.it:/path/to/data/ /local/destination/

3. Via SFTP Client

For a graphical interface to download files, see the dedicated guide:

👉 SFTP File Transfer Clients - Step-by-step instructions for: - Cyberduck (Windows, macOS) - FileZilla (Windows, macOS, Linux) - WinSCP (Windows)

Best Practices

  1. Check data integrity before deleting from the cluster
  2. Verify file sizes match expectations
  3. Use checksums (MD5/SHA256) to verify transfers
  4. Keep multiple backups of important data
  5. Document your data with metadata files

Data Retention Policy

[To be completed with specific retention policies]

  • Raw sequencing data: Retained for XX days
  • Processed data: User responsibility
  • Contact administrators if you need extended retention

Support

For questions about accessing or retrieving NGS data:

Last Updated: October 2025