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Updated: Jun 8, 2026

Unbiased Deep Sequencing of RNA Viruses from Clinical Samples

Unbiased Deep Sequencing of RNA Viruses from Clinical Samples

Published on: July 2, 2016

LAPIS is a fast web API for massive open virus sequencing data.

Chaoran Chen^1,2, Alexander Taepper^3,4, Fabian Engelniederhammer⁵

¹Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland. chaoran.chen@bsse.ethz.ch.

BMC Bioinformatics

|June 5, 2023

Summary

This summary is machine-generated.

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.

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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.