WisePulse¶

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

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.

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

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 Links¶

API Documentation¶

Service	Swagger UI
LAPIS COVID	lapis.wasap.genspectrum.org/covid/swagger-ui/index.html
LAPIS RSV-A	lapis.wasap.genspectrum.org/rsva/swagger-ui/index.html