Welcome to LAPIS
What is LAPIS?
Section titled “What is LAPIS?”LAPIS (Lightweight API for Sequences) is an open-source HTTP API for querying large collections of pathogen genome sequences. It is built for researchers, public health analysts and developers who need to filter, aggregate or download genomic data programmatically.
Under the hood, LAPIS delegates storage and fast filter execution to SILO, a purpose-built sequence database.
Known instances
Section titled “Known instances”LAPIS is deployed in a number of production systems:
- CoV-Spectrum and GenSpectrum are interactive dashboards for analyzing virus variants and mutations, backed by a LAPIS instance over INSDC and Pathoplexus data.
- Loculus is an open-source software for managing and sharing microbial genome data that uses LAPIS and SILO as its query engine. Production Loculus deployments include Pathoplexus, an initiative to facilitate sharing of genetic sequencing data for human viruses of public health importance.
- W-ASAP uses a LAPIS instance for wastewater sequencing data, supporting queries over mutation abundances from Swiss wastewater samples.
If you are operating a public LAPIS instance and want it to be listed here, please open an issue on GitHub.
Citation
Section titled “Citation”If you use LAPIS in your work, please cite:
Chen, C., Taepper, A., Engelniederhammer, F., Kellerer, J., Roemer, C. & Stadler, T. “LAPIS is a fast web API for massive open virus sequencing data” BMC Bioinformatics (2023); doi: 10.1186/s12859-023-05364-3