The CGE Tool Box

Mette Voldby Larsen, Katrine Grimstrup Joensen, Ea Zankari, Johanne Ahrenfeldt, Oksana Lukjancenko, Rolf Sommer Kaas, Louise Roer, Pimlapas Leekitcharoenphon, Dhany Saputra, S. Cosentino, Martin Christen Frølund Thomsen, Jose Luis Bellod Cisneros, Vanessa Isabell Jurtz, Simon Rasmussen, Thomas Nordahl Petersen, Henrik Hasman, Thomas Sicheritz-Pontén, Frank Møller Aarestrup, Ole Lund

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

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.
Original languageEnglish
Title of host publicationApplied Genomics of Foodborne Pathogens
Place of PublicationSwitzerland
PublisherSpringer
Publication date2017
Pages65-90
Chapter5
DOIs
Publication statusPublished - 2017

Keywords

  • Life Sciences
  • Food Microbiology
  • Food Science
  • Bioinformatics
  • Microbial Genetics and Genomics
  • Applied Microbiology
  • Whole genome sequencing
  • Web-services

Cite this

Larsen, M. V., Joensen, K. G., Zankari, E., Ahrenfeldt, J., Lukjancenko, O., Kaas, R. S., ... Lund, O. (2017). The CGE Tool Box. In Applied Genomics of Foodborne Pathogens (pp. 65-90). Switzerland: Springer. https://doi.org/10.1007/978-3-319-43751-4_5