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The CGE Tool Box

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Applied Genomics of Foodborne Pathogens

Part of the book series: Food Microbiology and Food Safety ((RESDEV))

Abstract

As whole genome sequence data of microorganisms are becoming easily accessible and cheap to produce, a transformation of the traditional methods used for typing, phenotyping and phylogenetic analysis of microorganisms is on the way. Following the anticipation that most clinical microbiological and food safety laboratories will soon have a sequencer in use on a daily basis, there is a growing need for easy-to-use bioinformatics methods that can quickly convert the sequence data into useful information on, e.g., the type of bacteria, whether it is resistant towards any types of antibiotics, and whether it is part of an outbreak. The Center for Genomic Epidemiology, which is located at the Technical University of Denmark, has since its beginning in 2010 developed such bioinformatics methods and made them freely available as web-services. These web-services and their use is the focus of this chapter.

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Notes

  1. 1.

    VCF (Variant Call Format) files specify a type of text files used for storing sequence variation.

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Acknowledgements

The Center for Genomic Epidemiology at the Technical University of Denmark is funded by grant 09-067103/DSF from the Danish Council for Strategic Research.

Author information

Authors and Affiliations

  1. Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark

    Mette Voldby Larsen, Ea Zankari, Johanne Ahrenfeldt, Oksana Lukjancenko, Dhany Saputra, Martin Christen Frølund Thomsen, Jose Luis Bellod Cisneros, Vanessa Jurtz, Simon Rasmussen, Thomas Nordahl Petersen, Thomas Sicheritz-Ponten & Ole Lund

  2. Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark

    Katrine G. Joensen, Henrik Hasman & Frank M. Aarestrup

  3. National Food Institute, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark

    Ea Zankari, Oksana Lukjancenko, Rolf Sommer Kaas, Louise Roer & Pimlapas Leekitcharoenphon

  4. Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan

    Salvatore Cosentino

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  1. Mette Voldby Larsen
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  11. Martin Christen Frølund Thomsen
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  18. Frank M. Aarestrup
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  19. Ole Lund
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Corresponding author

Correspondence to Mette Voldby Larsen .

Editor information

Editors and Affiliations

  1. Center for Food Safety, University of Georgia, Griffin, Georgia, USA

    Xiangyu Deng

  2. Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA

    Henk C. den Bakker

  3. National Food Institute, Technical University of Denmark, Copenhagen, Denmark

    Rene S. Hendriksen

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Larsen, M.V. et al. (2017). The CGE Tool Box. In: Deng, X., den Bakker, H., Hendriksen, R. (eds) Applied Genomics of Foodborne Pathogens. Food Microbiology and Food Safety(). Springer, Cham. https://doi.org/10.1007/978-3-319-43751-4_5

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