DivBase is a service built and maintained by SciLifeLab Data Centre that enables life science researchers at Swedish institutions and their collaborators to manage, explore, and query genomic variants in VCF format alongside associated sample metadata. The service provides a secure platform for managing genomic variants and metadata files for non-human and non-sensitive data.
Note
DivBase is currently in pre-release for a limited number of users. We are actively seeking feedback to help shape the service. If you would like to be involved in testing or have suggestions, please reach out at dsn-eb@scilifelab.se or open a GitHub Issue.
- Join an existing project: Create an account at the DivBase web interface and ask your project manager to add you.
- Start your own project: Reach out to us at dsn-eb@scilifelab.se.
- Store all your variant data and metadata in one place - a single, centralised store for all VCF files and sample metadata from your research project.
- Collaborate and share data with colleagues and collaborators, with full control over who has access to what.
- Query across all your VCF files at once, or narrow down to a subset of your choosing.
- Filter on variant data and sample metadata in the same query - no need to join results together manually.
- Integrate the system into your pipelines and HPC jobs - use DivBase programmatically wherever your workflow needs it.
- Keep all files under version control and backed up.
- Checkpoint the state of your project's files to refer back to at a later date - making your research more easily reproducible.
For guides, tutorials, and command references, visit our documentation website.
To manage files, submit queries, and interact with DivBase, install our command line tool divbase-cli using uv or pipx:
uv tool install divbase-cli
# or with pipx
pipx install divbase-cliFor detailed instructions and alternative methods, see our Installation Guide.
Tip
Go to our documentation website for the proper Quick Start Guide.
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Create an Account: Sign up at the DivBase Web Interface.
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Configure: Add your project to your CLI config and set it as default:
divbase-cli config add MY_PROJECT_NAME --default
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Login:
divbase-cli auth login your.email@example.com
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Upload Data and sync your data
divbase-cli files upload data/my_metadata.tsv divbase-cli files upload data/my_samples/*.vcf.gz divbase-cli dimensions update -
Run a Query:
# Filter samples based on metadata and subset a chromosomal region in one divbase-cli query vcf \ --tsv-filter "Area:Northern Portugal" \ --command "view -r 21:15000000-25000000"
This will submit a job to DivBase and once the job is complete, a new vcf.gz file containing the subset of data you requested will be available for download/streaming in your downstream analysis.
- Need help? Contact us at dsn-eb@scilifelab.se or open a GitHub Issue.
- Found a bug? Please report it on our GitHub Issues page.
We welcome contributions! See our Contributing and Developer Setup guides to get started. Feel free to reach out if you have questions or aren't sure where to start.