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    29 repositories

    • LAPIS

      Public
      An API, a query engine, and a database schema for genomic sequences; currently with a focus on SARS-CoV-2
      researchgenomicsepidemiologycovid-19sars-cov-2
      Kotlin
      •
      GNU Affero General Public License v3.0
      •6•30•66•11•Updated Feb 26, 2026Feb 26, 2026

    • LAPIS-SILO

      Public
      High-performance analytical database for sequence alignment data
      C++
      •
      GNU Affero General Public License v3.0
      •5•18•97•9•Updated Feb 26, 2026Feb 26, 2026

    • evobench

      Public
      Tool to produce, store and analyze performance data of SILO and perhaps later LAPIS?
      Rust
      •
      Other
      •1•1•11•1•Updated Feb 25, 2026Feb 25, 2026

    • silo-benchmark-ci

      Public
      SILO benchmarking CI system setup
      Shell
      •0•0•1•0•Updated Feb 25, 2026Feb 25, 2026

    • dashboards

      Public
      TypeScript
      •
      GNU Affero General Public License v3.0
      •0•7•93•15•Updated Feb 25, 2026Feb 25, 2026

    • dashboard-components

      Public
      TypeScript
      •
      GNU Affero General Public License v3.0
      •0•4•65•6•Updated Feb 23, 2026Feb 23, 2026

    • LAPIS-SILO-e2e

      Public
      TypeScript
      •1•1•10•1•Updated Feb 23, 2026Feb 23, 2026

    • influenza-override-groups

      Public
      This directory creates a JSON that contains the mapping of Influenza genbank assemblies to segment accessions
      Python
      •0•0•5•0•Updated Feb 16, 2026Feb 16, 2026

    • nextclade-datasets

      Public
      0•0•0•1•Updated Jan 28, 2026Jan 28, 2026

    • cov-spectrum-website

      Public
      A web platform to detect and analyze variants of SARS-CoV-2
      researchgenomicsepidemiologycovid-19sars-cov-2cov-spectrum
      TypeScript
      •
      GNU General Public License v3.0
      •15•61•86•16•Updated Jan 15, 2026Jan 15, 2026

    • api-query

      Public
      Somewhat generic utility for querying some API(s)
      Rust
      •1•0•0•0•Updated Dec 14, 2025Dec 14, 2025

    • locksafely

      Public
      Better locks via lock files for shell scripts
      Shell
      •1•0•0•0•Updated Nov 20, 2025Nov 20, 2025

    • docker-autoheal

      Public
      Monitor and restart unhealthy docker containers.
      Shell
      •
      MIT License
      •253•0•0•0•Updated Nov 19, 2025Nov 19, 2025

    • .github

      Public
      0•0•0•0•Updated Sep 21, 2025Sep 21, 2025

    • lineage-definitions

      Public
      Python
      •0•0•1•0•Updated Sep 15, 2025Sep 15, 2025

    • ingest

      Public
      Kotlin
      •0•1•0•0•Updated Sep 2, 2025Sep 2, 2025

    • silo-benchmark-runner

      Public archive
      Running evobench benchmarks on LAPIS-SILO
      0•0•0•0•Updated Jul 7, 2025Jul 7, 2025

    • WISE-mut-freq-data-uploader

      Public
      This repo includes a script to upload waste water virus mutation frequency data, produced by pangolin automation running v-pipe.
      Python
      •0•1•0•0•Updated Apr 17, 2025Apr 17, 2025

    • firewall

      Public
      Rust
      •1•0•0•0•Updated Apr 15, 2025Apr 15, 2025

    • loculus-addons

      Public
      JavaScript
      •0•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • cov-spectrum-server

      Public
      The server part of CoV-Spectrum
      cov-spectrum
      Kotlin
      •
      GNU General Public License v3.0
      •3•6•1•3•Updated Jan 18, 2025Jan 18, 2025

    • genspectrum-homepage

      Public archive
      HTML
      •0•1•0•0•Updated Dec 21, 2024Dec 21, 2024

    • loculus-config

      Public
      Shell
      •0•0•0•0•Updated Sep 20, 2024Sep 20, 2024

    • lapisR

      Public
      R
      •0•2•1•0•Updated Apr 4, 2024Apr 4, 2024

    • genspectrum-chat-conversations

      Public
      0•0•0•0•Updated Jun 19, 2023Jun 19, 2023

    • discussions

      Public
      0•0•0•0•Updated Apr 9, 2023Apr 9, 2023

    • cov-spectrum-ppretty

      Public
      R
      •
      GNU General Public License v3.0
      •0•1•10•0•Updated Dec 17, 2022Dec 17, 2022

    • mpox-spectrum-website

      Public archive
      TypeScript
      •1•4•8•0•Updated Dec 17, 2022Dec 17, 2022

    • cov-spectrum-docs

      Public archive
      cov-spectrum
      1•2•0•0•Updated Nov 3, 2021Nov 3, 2021