Related Experiment Video
Updated: Jun 8, 2026
09:36
Unbiased Deep Sequencing of RNA Viruses from Clinical Samples
Published on: July 2, 2016
17.1K
LAPIS is a fast web API for massive open virus sequencing data
Chaoran Chen1,2, Alexander Taepper3,4, Fabian Engelniederhammer5
1Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland. chaoran.chen@bsse.ethz.ch.
BMC Bioinformatics
|June 5, 2023
Summary
Genomic sequencing data is crucial for tracking pathogen spread. The Lightweight API for Sequences (LAPIS) provides fast, efficient access and analysis of this vital data for genomic epidemiology.
Area of Science:
- Genomics
- Bioinformatics
- Epidemiology
Background:
- Genomic sequencing data is essential for tracking infectious disease outbreaks like SARS-CoV-2 and mpox.
- Rapid generation of sequence data necessitates efficient access and processing tools.
Purpose of the Study:
- To develop a system for rapid retrieval and analysis of large-scale genomic sequencing data.
- To address the challenge of accessing and processing vast amounts of pathogen sequence data.
Main Methods:
- Developed the Lightweight API for Sequences (LAPIS), a REST API.
- Utilized a novel in-memory database engine for high-speed data processing.
- Implemented complex query capabilities for mutations and metadata.
Main Results:
- LAPIS demonstrated high speed and throughput, processing over 20 million requests with millisecond response times for 14.5 million SARS-CoV-2 sequences.
- The system supports complex, mutation- and metadata-based queries and data aggregation.
- LAPIS serves as the backend for public dashboards tracking SARS-CoV-2 and mpox.
Conclusions:
- LAPIS enhances genomic data accessibility through an optimized database and web API.
- It is designed as a versatile backend for dashboards and analyses.
- Potential for integration with major databases like GenBank exists.
