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Services

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

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

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

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

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

  • Fast prediction of bacterial taxonomy.
    Reads2Type

  • Fast DNA search engine.
    Tapir

Phylogeny:
  • SNPs phylogenetic tree from assembled genomes or sets of reads.
    snpTree

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


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CGE
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.


News

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...

Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads
January 2014

Cheap dna sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their dna. Link to article...

Pathogenic bacteria identified and described directly from clinical samples within a day
December 2013

The CGE project has demonstrated how, within the space of a single day, pathogenic bacteria can be identified and described directly from clinical samples. In the long term, this will help doctors treat patients more quickly with the right medicine, thus reducing periods of illness and saving lives. 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