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    120 repositories

    • sofi_core

      Public
      Python
      •1•1•3•30•Updated Aug 22, 2025Aug 22, 2025

    • sofi_core_gitops

      Public
      GitOps configuration for the sofi_core Kubernetes cluster
      2•0•0•0•Updated Aug 21, 2025Aug 21, 2025

    • bifrost_chewbbaca

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Aug 19, 2025Aug 19, 2025

    • ssi_analysis_utility

      Public
      Package for the species specific analysis WP6 MicrobeSeq
      Python
      •
      MIT License
      •0•2•14•2•Updated Aug 19, 2025Aug 19, 2025

    • uQCme

      Public
      Microbial Quality Control Web Application
      Python
      •0•0•0•0•Updated Aug 14, 2025Aug 14, 2025

    • bifrost_cge_mlst

      Public
      Bifrost Component: CGE MLST - Runs kma on a mlst DB using paired reads
      Python
      •
      MIT License
      •0•0•1•0•Updated Aug 11, 2025Aug 11, 2025

    • bifrost_sp_ecoli

      Public
      Ecoli related analysis for the SOFI platform.
      typingbifrostecolisofi
      Python
      •0•0•0•0•Updated Aug 6, 2025Aug 6, 2025

    • aedseo

      Public
      Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels
      surveillance-systemsonset-detectionburden-of-diseaseepidemic-modelepidemic-modelling
      R
      •
      Other
      •0•1•3•1•Updated Jul 14, 2025Jul 14, 2025

    • MicrobeSeq-Denmark

      Public
      Location for SSI's microbial surveillance pipelines
      documentationmicrobeseq
      SCSS
      •0•0•1•0•Updated Jun 26, 2025Jun 26, 2025

    • bifrost_bridge

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 19, 2025Jun 19, 2025

    • ubio_autobox

      Public
      Tool for running microbial bioinformatics routine automation.
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 16, 2025Jun 16, 2025

    • bio_api

      Public
      REST API for triggering bioinformatic calculations from SOFI
      Python
      •0•1•0•0•Updated Jun 6, 2025Jun 6, 2025

    • ssi_analysis_result_parsers

      Public
      Data wranglers for species specific pipelines to extract results for downstream databases
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 22, 2025May 22, 2025

    • bifrost_reporter

      Public
      Bifrost reporter for EQA
      Python
      •
      MIT License
      •1•0•0•1•Updated May 22, 2025May 22, 2025

    • bifrost_reporter_lebc

      Public
      Bifrost reporter for EQA
      Python
      •
      MIT License
      •1•0•0•0•Updated May 9, 2025May 9, 2025

    • cdiff_fbi

      Public
      Typing of Clostridioides difficile isolates using NGS data (reads and contigs) based on tandem repeat loci (TR6, TR10), and toxin genes (cdtA, cdtB, tcdA, tcdB, tcdC).
      typingtandem-repeatsfbitoxinscdiff
      ASP.NET
      •
      MIT License
      •0•1•0•0•Updated May 1, 2025May 1, 2025

    • microbeseq_nbdev_augment

      Public
      Files to assist in setup of nbdev
      templategetting-startednbdev
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Apr 7, 2025Apr 7, 2025

    • diseasystore

      Public
      R package that provides a feature store tailored towards disease modelling
      R
      •
      GNU General Public License v3.0
      •2•4•6•1•Updated Apr 1, 2025Apr 1, 2025

    • AEF-DDF

      Public
      R
      •0•1•1•0•Updated Apr 1, 2025Apr 1, 2025

    • SCDB

      Public
      R package for maintaining data bases with slowly-changing-dimensions
      R
      •
      GNU General Public License v3.0
      •3•6•6•2•Updated Mar 31, 2025Mar 31, 2025

    • epi_point

      Public
      S epidermidis pointfinder
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 26, 2025Mar 26, 2025

    • bifrost_run_launcher

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 24, 2025Mar 24, 2025

    • microreact_integration

      Public
      Python code for integrating with Microreact
      Python
      •
      MIT License
      •1•8•0•1•Updated Mar 20, 2025Mar 20, 2025

    • sofi-mr-server

      Public
      JavaScript
      •
      MIT License
      •1•0•0•5•Updated Mar 13, 2025Mar 13, 2025

    • GeneSNPdetector

      Public
      Python
      •0•0•0•0•Updated Mar 5, 2025Mar 5, 2025

    • ssi_pingme

      Public
      notificationstoolnbdev
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 4, 2025Mar 4, 2025

    • diseasy

      Public
      R
      •0•6•16•2•Updated Feb 28, 2025Feb 28, 2025

    • rmlst

      Public
      Python
      •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

    • bifrost_sp_cdiff

      Public
      Cdiff related analysis for the SOFI platform.
      typingbifrostsoficdiff
      Python
      •0•0•0•0•Updated Feb 24, 2025Feb 24, 2025

    • porA

      Public
      Scripts for porA amplicon analysis
      Python
      •0•0•0•0•Updated Feb 21, 2025Feb 21, 2025