WisePulse

WISE Loculus with V-Pipe – Infrastructure for start-to-end viral wastewater analysis

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About

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)

Major Goals

• Cluster to Browser: Brought downstream exploratory analysis from exclusive, high barrier-to-entry cluster-based workflows to user-friendly, simple browser-based workflows

• 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

• 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

• Isolated to Integrated: First time wastewater data can be analyzed on the fly with the latest clinical variant definitions without manual work

Current Features

• Loculus instance for easy data sharing and collaboration
• Multi-virus srSILO API for querying amplicon sequence data (SARS-CoV-2, RSV-A)

Live Instances

• Mutational Analysis Dashboards: genspectrum.org/swiss-wastewater
• Swiss Wastewater Viral Alignment Database: db.wasap.genspectrum.org
• API Swagger UI: COVID | RSV-A

Data Processing Pipeline (external)

Upstream data processing is handled separately:

• NGS processing via V-pipe
• Database ingestion with sr2silo from V-pipe alignment outputs

Roadmap

• Expand to more viruses
• Raw data submission & V-pipe pipeline integration
• On-demand exploratory analysis tools

Quick Start

# One-time setup: install dependencies, build Rust tools, deploy configs, create venv
ansible-playbook playbooks/srsilo/setup.yml -i inventory.ini --become --ask-become-pass

# Set up the daily systemd timer
ansible-playbook playbooks/srsilo/setup-timer.yml -i inventory.ini --become --ask-become-pass

# Run the pipeline manually
/opt/srsilo/venv/bin/python -m pipeline --config /opt/srsilo/pipeline.yml

The data pipeline lives in srsilo-updater/ — a Python package that wraps the Rust fetch/sort/merge binaries and manages the SILO Docker containers. See its README for local dev instructions.

Documentation

See the full documentation for installation, configuration, and operations guides.