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LAPIS (version 0.3.10)

Introduction

LAPIS (Lightweight API for Sequences) is a webservice for querying genomic sequences. It is designed for pathogen data to answer genomic epidemiological questions. Main features include:

  • Data retrieval: You can download sequences, metadata, alignments, translations, and annotation data.
  • Data aggregation: You can flexibly group and aggregate sequences (e.g., to find out the number of sequences per country over time)
  • Powerful filters: You can filter by metadata and combinations of mutations. It is possible to specify complex filter conditions using Boolean logic.
  • Easy to use: It is a simple HTTP/REST API (application programming interface). For most cases, you can query it just by typing a URL into your browser. It can also be called from any programming language.
  • Many output formats: You can download the metadata and aggregated data as JSON, CSV, or TSV. Sequences are provided as FASTA.
  • Very fast: LAPIS was originally developed to query SARS-CoV-2 sequences and, therefore, capable to process millions of sequences efficiently. It uses SILO as its data query engine.

LAPIS is open source and available on GitHub. Feel free to report any issues there. Contributions are welcome.

You can find background information of LAPIS in the following publication. For up-to-date information, please rely on this documentation.

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

Hosting LAPIS Yourself

LAPIS is designed to be configurable to make analysis of genomic data available to a wide range of users. It is possible to host your own instance of LAPIS and to configure it to your needs. We want to make it as easy as possible to set up your own instance of LAPIS. If you have any trouble, feel free to reach out to us.