WisePulse is an end-to-end infrastructure for viral wastewater surveillance, combining Loculus for sequence data management with LAPIS-SILO, a high-performance genomic database – here deployed for the first time to Short-Read / amplicon sequences. It enables real-time querying and visualization of viral genomic data from wastewater samples.
Built with Ansible for infrastructure-as-code, enabling quick redeployment to other institutions and environments.
Demo: Watch on YouTube (starts at 7:00)
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Cluster to Browser: Brought downstream exploratory analysis from exclusive, high barrier-to-entry cluster-based workflows to user-friendly, simple browser-based workflows
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Days to Minutes: Simplified exploratory analysis beyond the regular processing reports produced by the WISE Consortium from days waiting for requests served by few with data access to self-serving
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Expert-only to Community Access: Direct access to data allows for community access—not just those with data access and expert bioinformatics knowledge—to explore, catering for virologists and phylogeneticists
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Isolated to Integrated: First time wastewater data can be analyzed on the fly with the latest clinical variant definitions without manual work
- Loculus instance for easy data sharing and collaboration
- Multi-virus srSILO API for querying amplicon sequence data (SARS-CoV-2, RSV-A)
- Mutational Analysis Dashboards: genspectrum.org/swiss-wastewater
- Swiss Wastewater Viral Alignment Database: db.wasap.genspectrum.org
- API Swagger UI: COVID | RSV-A
Upstream data processing is handled separately:
- Expand to more viruses
- Raw data submission & V-pipe pipeline integration
- On-demand exploratory analysis tools
# One-time setup
ansible-playbook playbooks/srsilo/setup.yml -i inventory.ini --become --ask-become-pass
# Run pipeline
ansible-playbook playbooks/srsilo/update-all-viruses.yml -i inventory.ini --become --ask-become-passSee the full documentation for installation, configuration, and operations guides.