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

doi:10.1007/978-3-319-43751-4_5

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 proceeding › Book chapter › Research › peer-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 language	English
Title of host publication	Applied Genomics of Foodborne Pathogens
Place of Publication	Switzerland
Publisher	Springer
Publication date	2017
Pages	65-90
Chapter	5
DOIs	https://doi.org/10.1007/978-3-319-43751-4_5
Publication status	Published - 2017

Keywords

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

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10.1007/978-3-319-43751-4_5

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Larsen, M. V., Joensen, K. G., Zankari, E., Ahrenfeldt, J., Lukjancenko, O., Kaas, R. S., Roer, L., Leekitcharoenphon, P., Saputra, D., Cosentino, S., Thomsen, M. C. F., Bellod Cisneros, J. L., Jurtz, V. I., Rasmussen, S., Petersen, T. N., Hasman, H., Sicheritz-Pontén, T., Aarestrup, F. M., & Lund, O. (2017). The CGE Tool Box. In Applied Genomics of Foodborne Pathogens (pp. 65-90). Springer. https://doi.org/10.1007/978-3-319-43751-4_5

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Larsen, MV, Joensen, KG, Zankari, E, Ahrenfeldt, J, Lukjancenko, O, Kaas, RS, Roer, L, Leekitcharoenphon, P, Saputra, D, Cosentino, S, Thomsen, MCF, Bellod Cisneros, JL, Jurtz, VI, Rasmussen, S, Petersen, TN, Hasman, H, Sicheritz-Pontén, T, Aarestrup, FM & Lund, O 2017, The CGE Tool Box. in Applied Genomics of Foodborne Pathogens. Springer, Switzerland, pp. 65-90. https://doi.org/10.1007/978-3-319-43751-4_5

TY - CHAP

T1 - The CGE Tool Box

AU - Larsen, Mette Voldby

AU - Joensen, Katrine Grimstrup

AU - Zankari, Ea

AU - Ahrenfeldt, Johanne

AU - Lukjancenko, Oksana

AU - Kaas, Rolf Sommer

AU - Roer, Louise

AU - Leekitcharoenphon, Pimlapas

AU - Saputra, Dhany

AU - Cosentino, S.

AU - Thomsen, Martin Christen Frølund

AU - Bellod Cisneros, Jose Luis

AU - Jurtz, Vanessa Isabell

AU - Rasmussen, Simon

AU - Petersen, Thomas Nordahl

AU - Hasman, Henrik

AU - Sicheritz-Pontén, Thomas

AU - Aarestrup, Frank Møller

AU - Lund, Ole

PY - 2017

Y1 - 2017

N2 - 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.

AB - 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.

KW - Life Sciences

KW - Food Microbiology

KW - Food Science

KW - Bioinformatics

KW - Microbial Genetics and Genomics

KW - Applied Microbiology

KW - Whole genome sequencing

KW - Web-services

U2 - 10.1007/978-3-319-43751-4_5

DO - 10.1007/978-3-319-43751-4_5

M3 - Book chapter

SP - 65

EP - 90

BT - Applied Genomics of Foodborne Pathogens

PB - Springer

CY - Switzerland

ER -

The CGE Tool Box

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