Are there any genomics analysis software tools that handle large file uploads and secure cross-team collaboration?

Yes. There are several genomics analysis platforms designed to handle large sequence/data uploads and support secure collaboration across teams. The best choice depends on whether you want a cloud-native platform, an enterprise collaboration environment, or an open-source/self-hosted option.

Common options

1. DNAnexus

• Built for large-scale genomics data
• Supports secure upload of very large files
• Role-based access control and team/project sharing
• Common in clinical, pharma, and research settings
• Good for regulated environments

2. Seven Bridges

• Cloud-based genomics platform
• Handles large datasets and workflow execution
• Strong collaboration features for teams
• Secure access controls and audit trails
• Often used for variant analysis, pipelines, and multi-user projects

3. Terra (Broad Institute)

• Designed for collaborative biomedical data analysis
• Good support for large datasets and reproducible workflows
• Workspace-based collaboration with permissions
• Popular in academic and consortium settings

4. BaseSpace Sequence Hub (Illumina)

• Useful if your data comes from Illumina instruments
• Supports upload, storage, analysis, and team sharing
• Good for sequencing workflows and integrated apps

5. Google Cloud / AWS genomics stacks

• Not a single app, but can be built into a secure collaborative environment
• Strong for large-file storage and access control
• Needs more configuration than turnkey platforms

6. Cavatica / open-source-style collaborative platforms

• More oriented toward research collaboration and workflow sharing
• Can support large files depending on deployment
• Good for teams needing reproducibility and controlled access

What to look for

For your use case, check that the platform includes:

• Multipart/resumable upload for big files
• Encryption in transit and at rest
• User/group permissions
• Audit logs
• Workspace or project-level sharing
• Workflow reproducibility
• Compliance support if needed (HIPAA, GDPR, etc.)

Best fits by scenario

• Enterprise / clinical genomics: DNAnexus, Seven Bridges
• Academic collaboration: Terra
• Illumina-centric labs: BaseSpace
• Highly customized infrastructure: AWS/GCP-based solutions

If you want, I can also give you a comparison table of these tools by price model, security, file size support, and collaboration features.