Statens Serum Institut

bifrost_dashboard

AD_staphylome_project

bifrost_amrfinderplus

bifrost_cge_virulencefinder

dash-scroll-up

Dash component to add custom button to scroll to the top of the page.

epidome

Databases, scripts and example data pertaining to the epidome. Subspecies classification of S. epidermidis based on amplicon sequencing.

flustrain

Consensus sequence generation and subtyping of influenza virus

Pig_truck_drivers_Ingham_et_al

read_filtering

Scripts for cleaning of raw read files, human read filtering etc.

tsvanon

Script for anonymizing tsv data

ansible-conda-env

ansible-grafana-podman

Ansible role for installing and configuring Grafana to run in container.

ansible-miniconda

ansible-podman-container-systemd

creates systemd files and creates containers using podman

ansible-prometheus-podman

Ansible role for installing and configuring Prometheus to run in container.

bifrost_ariba_mlst

Bifrost Component: Ariba MLST - Runs MLST against paired reads using ARIBA

bifrost_ariba_plasmidfinder

Bifrost Component: Ariba PlasmidFinder - Runs Ariba against PlasmidFinder DB using paired reads.

bifrost_ariba_resfinder

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

bifrost_ariba_virulencefinder

Bifrost Component: Ariba Virulencefinder - Runs Ariba on virulencefinder DB against paired reads.

bifrost_run_launcher

bifrostapi

Contains the python library for connecting with the bifrost database. Used by bifrost and beone dashboards.

calc-script-demux_illumina

calc-script-find_run_diff

Covid_variant_calling

epidome_2022

Epidome databases and scripts for 2022 update

index2rc

Creates illumina samplesheet with the reverse complement of the second index (index2).

pipeline-from-aalborg

Bioinformatic pipelines used to assemble SARS-CoV-2 genomes from DK

prokka_roary_toolbox

Scripts for running prokka and roary on calc.

SARS-CoV-2-leader

SCCmec

SCCmec data, scripts and analysis