LAPIS

LAPIS provides programmatic RESTful API access and high-performance query and aggregation operations on large viral genomic sequencing datasets, including SARS-CoV-2 and mpox, to support genomic epidemiology and tracking of pathogen mutations and spread.

Key Features:

• Programmatic RESTful API: Exposes a RESTful web API for programmatic query and retrieval of sequencing records and associated metadata.
• High-Speed Data Processing: Uses an in-memory database engine to achieve high throughput; its SARS-CoV-2 instance processed over 20 million requests between January 25 and February 4, 2023 with mean response time 411 ms and median 1 ms.
• Support for Complex Queries: Enables mutation-based and metadata-driven queries for detailed selection and filtering of sequences.
• Aggregation Operations: Performs aggregation operations efficiently to summarize large-scale sequence and metadata information for epidemiological analyses.
• Scalability: Architected to handle very large datasets and high request volumes for population-scale viral sequencing data.
• Integration Potential: Designed for integration with external database platforms such as GenBank.

Scientific Applications:

• Genomic epidemiology: Facilitates rapid retrieval and summarization of viral sequences to inform transmission and outbreak analyses.
• Mutation surveillance: Supports tracking of mutations across SARS-CoV-2, mpox, and other viral sequences via mutation-based queries.
• Outbreak monitoring: Enables temporal and geographic aggregation of sequencing data to monitor spread during outbreaks.
• Pathogen evolution studies: Provides large-scale sequence access and aggregation necessary for analyses of viral evolution and lineage dynamics.

Methodology:

Implements a REST API framework optimized for speed backed by an in-memory database engine and supports mutation-based and metadata-driven queries plus aggregation operations for low-latency querying of large viral sequencing datasets.