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Pipeline: Phenotyping: Typing:
  • Multi Locus Sequence Typing (MLST) from an assembled genome or from a set of reads

  • PlasmidFinder identifies plasmids in total or partial sequenced isolates of bacteria.

  • Multi Locus Sequence Typing (MLST) from an assembled plasmid or from a set of reads

  • Core genome Multi Locus Sequence Typing (cgMLST) from a set of reads

  • Prediction of bacterial species using a fast K-mer algorithm.

  • Prediction of bacterial species using the S16 ribosomal DNA sequence.

  • Prediction of serotypes in total or partial sequenced isolates of E. coli.

  • SeqSero predicts the Salmonella serotype of either the pre-assembled or raw read sequence data provided to the service.

  • spaTyper predicts the S. aureus spa type.

  • FimTyper predicts the E. coli Fim type.

  • CHTyper predicts the E. coli FimH type and FumC type.

  • CSI Phylogeny calls SNPs, filters the SNPs, does site validation and infers a phylogeny based on the concatenated alignment of the high quality* SNPs.

  • NDtree constructs phylogenetic trees from Single-End or Pair-End FASTQ files.

  • Evergreen generates a forest of constantly updated phylogenetic trees with publicly available whole-genome sequencing data from foodborne, bacterial isolates that were deposited in the short sequencing read archives (NCBI SRA/ENA).

  • MyKMAfinder performs typing or pheno typing using KMA based on a user defined database

  • MyDbFinder performs typing or pheno typing using blast based on a user defined database

  • MyKmerFinder performs typing or pheno typing using Kmers based on a user defined database

  • The DeHumanizer web-server is a tool for human filtering based on the method described by Zhang et al.




Welcome to the Center for Genomic Epidemiology

The cost of sequencing a bacterial genome is $50 and is expected to decrease further in the near future and the equipment needed cost less than $150 000. Thus, within a few years all clinical microbiological laboratories will have a sequencer in use on a daily basis. The price of genome sequencing is already so low that whole genome sequencing will also find worldwide application in human and veterinary practices as well as many other places where bacteria are handled. In Denmark alone this equals more than 1 million isolates annually in 15-20 laboratories and globally up to 1-2 billion isolates per year. The limiting factor will therefore in the future not be the cost of the sequencing, but how to assemble, process and handle the large amount of data in a standardized way that will make the information useful, especially for diagnostic and surveillance.

The aim of this center is to provide the scientific foundation for future internet-based solutions where a central database will enable simplification of total genome sequence information and comparison to all other sequenced including spatial-temporal analysis. We will develop algorithms for rapid analyses of whole genome DNA-sequences, tools for analyses and extraction of information from the sequence data and internet/web-interfaces for using the tools in the global scientific and medical community. The activity is being expanded to also include other microorganisms, such as vira and parasites as well as metagenomic samples.


New article: Rapid and precise alignment of raw reads against redundant databases with KMA
September 2018

Link to article....

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

Link to article....

What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?
December 2015

Link to article....

WGS typing is a superior alternative to conventional typing strategies
August 2015

In combination with other available WGS typing tools, E. coli serotyping can be performed solely from WGS data, providing faster and cheaper typing than current routine procedures. Link to article....

Introduction to microbial whole genome sequencing and analysis for clinical microbiologist
April 2015

We offer clinical microbiologists the possibility to learn how to use the tools for e.g. typing, identifying plasmids, antibiotic resistance and virulence genes and for phylogenetic analysis. Sign up....

Consortium to combat infectious disease outbreaks
January 2015

The COMPARE project has been funded with 20 million Euros from the EU. The Consortium consists of 29 partners with multidisciplinary expertise in human health, animal health and food safety. Read more....

Benchmarking of Methods for Genomic Taxonomy
April 2014

How to optimally determine taxonomy from whole genome sequences. Link to article...

CGE tools applied for bacteriophage characterization
March 2014

Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences. Link to article...

Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica
March 2014

We evaluated WGS for outbreak detection of Salmonella enterica including different approaches for analyzing and comparing with a traditional typing, PFGE. Link to article...

Global Microbial Identifier
December 2012

The initiative 'Global Microbial Identifier' focuses on the use of genome sequencing techniques in a global system for microbiological identification and epidemiological surveillance. Visit the homepage for further information

Copyright DTU 2011 / All rights reserved
Center for Genomic Epidemiology, DTU, Kemitorvet, Building 204, 2800 Kgs. Lyngby, Denmark
Contact: Vibeke Dybdahl Hammer, Telephone: +45 3588 6420, E-mail: vdha@food.dtu.dk
Funded by: The Danish Council for Strategic Research