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DivBase v0.1.0

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@RMCrean RMCrean released this 07 Oct 13:14
v0.1.0
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RMCrean Rory Crean
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Learn about vigilant mode.

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.

This is the first release of DivBase for external users. DivBase is currently being tested by a limited number of users, so expect features, commands and documentation to change in upcoming releases as we incorporate feedback.

DivBase allows you to

  • 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.

Getting started

  1. Get access: DivBase is currently only open to a limited group of test users. If you would like to take part in testing, email us at datacentre@scilifelab.se. If you have already been invited, create an account at the DivBase web interface and ask your project manager to add you to their project, using the email address you signed up with.

  2. Install divbase-cli, the command line tool for working with DivBase from your own computer or a HPC cluster:

    uv tool install divbase-cli
# or with pipx
# pipx install divbase-cli

  3. Follow the Quick Start Guide or try the tutorial Running a query on a public dataset.

The full documentation covers guides, tutorials and the CLI command reference.

Feedback

Please report bugs or suggestions by opening a GitHub Issue or emailing datacentre@scilifelab.se.

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