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
Larsen, Mette Voldby ; Joensen, Katrine Grimstrup ; Zankari, Ea ; Ahrenfeldt, Johanne ; Lukjancenko, Oksana ; Kaas, Rolf Sommer ; Roer, Louise ; Leekitcharoenphon, Pimlapas ; Saputra, Dhany ; Cosentino, S. ; Thomsen, Martin Christen Frølund ; Bellod Cisneros, Jose Luis ; Jurtz, Vanessa Isabell ; Rasmussen, Simon ; Petersen, Thomas Nordahl ; Hasman, Henrik ; Sicheritz-Pontén, Thomas ; Aarestrup, Frank Møller ; Lund, Ole. / The CGE Tool Box. Applied Genomics of Foodborne Pathogens. Switzerland : Springer, 2017. pp. 65-90
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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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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

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

Applied Genomics of Foodborne Pathogens. Switzerland : Springer, 2017. p. 65-90.

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

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 -

Larsen MV, Joensen KG, Zankari E, Ahrenfeldt J, Lukjancenko O, Kaas RS et al. The CGE Tool Box. In Applied Genomics of Foodborne Pathogens. Switzerland: Springer. 2017. p. 65-90 https://doi.org/10.1007/978-3-319-43751-4_5