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@ssi-dk Statens Serum Institut

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    141 repositories

    • sofi_core_gitops

      Public
      GitOps configuration for the sofi_core Kubernetes cluster
      2•0•0•0•Updated Aug 14, 2026Aug 14, 2026

    • sofi_core

      Public
      Python
      •4•2•3•29•Updated Aug 14, 2026Aug 14, 2026

    • MMASeq

      Public
      Package for the species specific analysis WP6 MicrobeSeq
      Python
      •
      MIT License
      •3•2•11•2•Updated Aug 14, 2026Aug 14, 2026

    • diseasystore

      Public
      R package that provides a feature store tailored towards disease modelling
      R
      •
      GNU General Public License v3.0
      •4•4•6•4•Updated Aug 14, 2026Aug 14, 2026

    • diseasy

      Public
      R
      •0•5•25•5•Updated Aug 14, 2026Aug 14, 2026

    • AEF-DDF

      Public
      R
      •0•1•1•0•Updated Aug 14, 2026Aug 14, 2026

    • SCDB

      Public
      R package for maintaining data bases with slowly-changing-dimensions
      R
      •
      GNU General Public License v3.0
      •4•8•14•7•Updated Aug 14, 2026Aug 14, 2026

    • uQCme

      Public
      Microbial Quality Control Web Application
      Python
      •
      MIT License
      •2•1•2•1•Updated Aug 13, 2026Aug 13, 2026

    • ubio_autobox

      Public
      Tool for running microbial bioinformatics routine automation.
      Python
      •
      MIT License
      •0•1•0•1•Updated Aug 13, 2026Aug 13, 2026

    • bifrost_chewbbaca

      Public
      Python
      •
      MIT License
      •2•1•0•1•Updated Aug 13, 2026Aug 13, 2026

    • aedseo

      Public template
      Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels
      surveillance-systemsonset-detectionburden-of-disease
      surveillance-systemsonset-detectionburden-of-diseaseepidemic-modelepidemic-modelling
      R
      •
      Other
      •1•1•2•1•Updated Aug 7, 2026Aug 7, 2026

    • bifrost_impl_sofi

      Public
      Python
      •1•0•1•0•Updated Aug 7, 2026Aug 7, 2026

    • bifrost_run_launcher

      Public
      Python
      •
      MIT License
      •1•0•1•0•Updated Aug 7, 2026Aug 7, 2026

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •4.1k•0•0•0•Updated Aug 6, 2026Aug 6, 2026

    • cgMLST_scheme_clean_check

      Public
      Scripts for cleaning cgMLST schemes and testing what size threshold would make sense for chewBBACA
      Python
      •0•0•0•0•Updated Aug 4, 2026Aug 4, 2026

    • bifrostlib

      Public
      Python API for bifrost
      Python
      •
      MIT License
      •2•0•3•0•Updated Aug 3, 2026Aug 3, 2026

    • landingzones

      Public
      A script for helping manage entry and exit points across machines for with cron.
      Python
      •1•1•2•0•Updated Jul 31, 2026Jul 31, 2026

    • bifrost_bridge

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Jul 30, 2026Jul 30, 2026

    • chewbbaca_fbi

      Public
      SSI FBI specific version of chewbbaca with slight alterations to allelecalling
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•14•Updated Jul 26, 2026Jul 26, 2026

    • sofi-mr-server

      Public
      JavaScript
      •
      MIT License
      •1•0•0•5•Updated Jun 30, 2026Jun 30, 2026

    • bifrost_amrfinderplus

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Jun 22, 2026Jun 22, 2026

    • ssiamb

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 17, 2026Jun 17, 2026

    • pmlst

      Public
      Modernized pMLST packaging and deployment workspace
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Jun 16, 2026Jun 16, 2026

    • sofi-requirements

      Public
      sofi requirements
      Shell
      •0•0•0•0•Updated Jun 16, 2026Jun 16, 2026

    • rmlst-cli

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 15, 2026Jun 15, 2026

    • bifrost_cge_resfinder

      Public
      Bifrost Component: CGE Resfinder - Runs kma on resfinder DB using paired reads
      Python
      •
      MIT License
      •2•0•0•0•Updated Jun 11, 2026Jun 11, 2026

    • ssi_analysis_utility_db

      Public
      Custom reference genomes used for species-specific analysis
      Shell
      •0•0•0•0•Updated Jun 9, 2026Jun 9, 2026

    • bio_api

      Public
      REST API for triggering bioinformatic calculations from SOFI
      Python
      •1•1•0•1•Updated Jun 5, 2026Jun 5, 2026

    • durep

      Public
      Disk usage report generator
      Python
      •
      MIT License
      •0•1•0•1•Updated Jun 4, 2026Jun 4, 2026

    • sequencer-sync

      Public
      Syncronize SSI sequencers with the server
      Rust
      •
      MIT License
      •0•0•0•1•Updated Jun 3, 2026Jun 3, 2026
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