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Statens Serum Institut (ssi-dk)

Statens Serum Institut

ssi-dk

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Location:Denmark

Home Page:https://www.ssi.dk/

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Statens Serum Institut's repositories

SCDB

R package for maintaining data bases with slowly-changing-dimensions

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GenEpi-BioTrain_Virtual_Training_7

All data used in the GenEpi-BioTrain Virtual Training 7 session on march 19-20, 2024

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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.

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microreact_integration

Python code for integrating with Microreact

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diseasy

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diseasystore

R package that provides a feature store tailored towards disease modelling

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AEF-DDF

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bifrost_chewbbaca

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ecoli_pathotypes

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microbeseq_nbdev_augment

Files to assist in setup of nbdev

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sofi_core

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bifrost_enterobase

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bifrost_salmonella_subspecies_dtartrate

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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

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BPS_FBI_FSC_VirulenceFinder

Bash scripts to run virulencefinder and serotypefinder in local settings on ecoli fasta and fastq.gz files.

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cdiff_fbi

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).

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Staphylococcal_nasal_occupancy

R scripts accompanying the manuscript "Staphylococcal occupancy within the human nasal microbiota" (Ingham et al.)

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BeONE-old-version

The BeONE project repo

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bifrost_cge_resfinder

Bifrost Component: CGE Resfinder - Runs kma on resfinder DB using paired reads

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bifrost_seqsero

Component for running seqsero in Bifrost

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bifrost_sp_cdiff

Cdiff related analysis for the SOFI platform.

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bifrost_sp_ecoli

Ecoli related analysis for the SOFI platform.

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bio_api

REST API for triggering bioinformatic calculations from SOFI

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bps_fbi_sp_ecoli

Ecoli species specific scripts in nbdev2 format.

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CD-MRG-Bruker

Scripts and documentation for Bruker software

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ecoli_fbi

Determines the serotype and virulence in Escherichia coli isolates using NGS data (reads) through kmer alignment.

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MicrobeSeq-Denmark

Location for SSI's microbial surveillance pipelines

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microbeseq_nbdev_example

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refseq_fastq_downloader

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sofi_core_gitops

GitOps configuration for the sofi_core Kubernetes cluster

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