Statens Serum Institut's repositories
GenEpi-BioTrain_Virtual_Training_7
All data used in the GenEpi-BioTrain Virtual Training 7 session on march 19-20, 2024
CD-MRG-PlatePlanner
Python package to create multi-well plate layouts for specimen sample data. Automatically distributes quality control samples according to scheme in config file.
diseasystore
R package that provides a feature store tailored towards disease modelling
microbeseq_nbdev_augment
Files to assist in setup of nbdev
microreact_integration
Python code for integrating with Microreact
bifrost_ssi_stamper
Bifrost Component: SSI Stamper - Runs SSI's QC check on samples using metrics generated from Assemblatron, Min Read Check and Whats my species
BPS_FBI_FSC_VirulenceFinder
Bash scripts to run virulencefinder and serotypefinder in local settings on ecoli fasta and fastq.gz files.
aedseo
Automated and Early Detection of Seasonal Epidemic Onset
AEF-DDF-diseasystoreFHM
Extends diseasystore with Swedish data from Folkhälsomyndigheten
AEF-DDF-flu-forecast-hub
European Influenza forecasting hub
BeONE-old-version
The BeONE project repo
bifrost_cge_resfinder
Bifrost Component: CGE Resfinder - Runs kma on resfinder DB using paired reads
bifrost_seqsero
Component for running seqsero in Bifrost
bio_api
REST API for triggering bioinformatic calculations from SOFI
bps_fbi_sp_ecoli
Species specific scripts for ecoli. Determines the serotype and virulence in ecoli through kmer alignment.
CD-MRG-Bruker
Scripts and documentation for Bruker software
CD-MRG-fakedata
Notebook showing how to create fake data for our typical case-control studies.
irida-uploader
Sequence file uploader for IRIDA
sofi_core_gitops
GitOps configuration for the sofi_core Kubernetes cluster