Center for Genomic Epidemiology

Welcome to the Center for Genomic Epidemiology

The use of sequencing technologies is currently transforming almost every aspect of biological science. In relation to infectious diseases, the advances are rapidly changing our scientific discoveries, as well as diagnostic and outbreak investigations. The ability to analyze sequencing data and take advantage of the rapid progress, is however, not equally distributed between institutions and countries.

The aim of the Center for Genomic Epidemiology (CGE) is to provide access to bioinformatics resources also for those with limited experience and thereby allow all countries, institutions and individuals to take advantage of the novel sequencing technologies. Doing so, we hope to facilitate more open data sharing around the world and provide more equal opportunities for all.

CGE is entirely non-commercial and operates a number of free online bioinformatics services. Funding is provided as core funding from the Technical University of Denmark (DTU) and from a range of public and private sources as listed below.

If you want to read more about us and our research activities, please visit the Global Surveillance website.


Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining

January 2023
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SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies

November 2022
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PlasmidHostFinder: prediction of plasmid hosts using random forest

April 2022
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ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes

January 2022
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MINTyper: an outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads

April 2021
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Automated download and clean-up of family specific databases for kmer-based virus identification

October 2020
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CRHP Finder, a webtool for the detection of clarithromycin resistance in Helicobacter pylori from whole-genome sequencing data

September 2020
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ResFinder 4.0 for predictions of phenotypes from genotypes

August 2020
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CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

April 2020
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Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform

March 2020
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Improved Resistance Prediction in Mycobacterium tuberculosis by Better Handling of Insertions and Deletions, Premature Stop Codons, and Filtering of Non-informative Sites

October 2019
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LRE-Finder, a Web tool for detection of the 23S rRNA mutations and the optrA, cfr, cfr(B) and poxtA genes encoding linezolid resistance in Enterococci from whole-genome sequences

March 2019
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Rapid and precise alignment of raw reads against redundant databases with KMA

September 2018
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Improved laboratory procedure and bioinformatics workflow for metagenomics-based identification of microorganisms: The workflow includes a curated reference genome database, reducing the identification of false-positives

April 2018
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