Skip to content

@ssi-dk Statens Serum Institut

Change the repository type filter

All

    Repositories list

    134 repositories

    • bifrost_bridge

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 24, 2026Apr 24, 2026

    • landingzones

      Public
      A script for helping manage entry and exit points across machines for with cron.
      Python
      •1•1•1•0•Updated Apr 24, 2026Apr 24, 2026

    • sofi_core

      Public
      Python
      •2•1•3•30•Updated Apr 23, 2026Apr 23, 2026

    • sequencer-sync

      Public
      Syncronize SSI sequencers with the server
      Rust
      •
      MIT License
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • Host_Element_Attribution_Pipeline

      Public
      contains pipeline developed by Jon during his thesis. Mostly a wrapper, with few additions and changes to original pipeline
      Python
      •
      MIT License
      •2•0•0•0•Updated Apr 22, 2026Apr 22, 2026

    • bifrost_sp_cdiff

      Public
      Cdiff related analysis for the SOFI platform.
      typingbifrostsofi
      typingbifrostsoficdiff
      Python
      •0•0•0•0•Updated Apr 22, 2026Apr 22, 2026

    • bifrost_seqsero

      Public
      Component for running seqsero in Bifrost
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 22, 2026Apr 22, 2026

    • bifrost_enterobase

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 22, 2026Apr 22, 2026

    • 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 Apr 22, 2026Apr 22, 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 Apr 21, 2026Apr 21, 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•9•Updated Apr 20, 2026Apr 20, 2026

    • sofi_core_gitops

      Public
      GitOps configuration for the sofi_core Kubernetes cluster
      2•0•0•0•Updated Apr 20, 2026Apr 20, 2026

    • MMASeq

      Public
      Package for the species specific analysis WP6 MicrobeSeq
      Python
      •
      MIT License
      •1•2•17•1•Updated Apr 17, 2026Apr 17, 2026

    • uQCme

      Public
      Microbial Quality Control Web Application
      Python
      •
      MIT License
      •2•1•2•0•Updated Apr 17, 2026Apr 17, 2026

    • durep

      Public
      Disk usage report generator
      Python
      •
      MIT License
      •0•0•0•2•Updated Apr 14, 2026Apr 14, 2026

    • ssiamb

      Public
      HTML
      •
      MIT License
      •0•0•0•4•Updated Apr 14, 2026Apr 14, 2026

    • Consensus

      Public
      Influenza consensus generation pipeline
      Julia
      •0•0•0•0•Updated Apr 8, 2026Apr 8, 2026

    • pregnancy-transcriptome

      Public
      Code accompanying the article: “An atlas of transcriptional dynamics in maternal blood over the course of healthy pregnancy” by Feenstra B, Hede FRD, Piening BD…
      R
      •
      MIT License
      •0•0•0•0•Updated Mar 30, 2026Mar 30, 2026

    • ssi_pingme

      Public
      notificationstoolnbdev
      notificationstoolnbdev
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • bifrost_salmonella_subspecies_dtartrate

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • bifrost_sp_ecoli

      Public
      Ecoli related analysis for the SOFI platform.
      typingbifrostecoli
      typingbifrostecolisofi
      Python
      •0•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • bifrost_chewbbaca

      Public
      Python
      •
      MIT License
      •1•1•0•1•Updated Mar 26, 2026Mar 26, 2026

    • bifrost_amrfinderplus

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • bifrost_cge_resfinder

      Public
      Bifrost Component: CGE Resfinder - Runs kma on resfinder DB using paired reads
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • bifrost_assemblatron

      Public
      Bifrost Component: Assemblatron - De-novo assembly of paired reads for QC and downstream Analysis purposes
      Python
      •
      MIT License
      •0•0•1•0•Updated Mar 26, 2026Mar 26, 2026

    • bifrost_ssi_stamper

      Public
      Bifrost Component: SSI Stamper - Runs SSI's QC check on samples using metrics generated from Assemblatron, Min Read Check and Whats my species
      Python
      •
      MIT License
      •0•0•4•0•Updated Mar 26, 2026Mar 26, 2026

    • bifrost_whats_my_species

      Public
      Bifrost Component: Whats My Species - Checks species of sample and whether it's correct or not against a kraken DB
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • bifrost_min_read_check

      Public
      Bifrost Component: Min Read Check - Checks that provided read files have a minimum number of reads for analysis
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • bifrost_run_launcher

      Public
      Python
      •
      MIT License
      •0•0•1•0•Updated Mar 26, 2026Mar 26, 2026

    • diseasy

      Public
      R
      •0•5•25•5•Updated Mar 20, 2026Mar 20, 2026
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.