  Background: Recent epidemic outbreaks such as the SARS-CoV-2 pandemic and the
mpox outbreak in 2022 have demonstrated the value of genomic sequencing data
for tracking the origin and spread of pathogens. Laboratories around the globe
generated new sequences at unprecedented speed and volume and bioinformaticians
developed new tools and dashboards to analyze this wealth of data. However, a
major challenge that remains is the lack of simple and efficient approaches for
accessing and processing sequencing data.
  Results: The Lightweight API for Sequences (LAPIS) facilitates rapid
retrieval and analysis of genomic sequencing data through a REST API. It
supports complex mutation- and metadata-based queries and can perform
aggregation operations on massive datasets. LAPIS is optimized for typical
questions relevant to genomic epidemiology. Using a newly-developed in-memory
database engine, it has a high speed and throughput: between 25 January and 4
February 2023, the SARS-CoV-2 instance of LAPIS, which contains 14.5 million
sequences, processed over 20 million requests with a mean response time of 411
ms and a median response time of 1 ms. LAPIS is the core engine behind our
dashboards on genspectrum.org and we currently maintain public LAPIS instances
for SARS-CoV-2 and mpox.
  Conclusions: Powered by an optimized database engine and available through a
web API, LAPIS enhances the accessibility of genomic sequencing data. It is
designed to serve as a common backend for dashboards and analyses with the
potential to be integrated into common database platforms such as GenBank.
