Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions : Nature Reviews Genetics : Nature Publishing Group

Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions : Nature Reviews Genetics : Nature Publishing Group

Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions

• W. Florian Fricke
• & David A. Rasko

• Affiliations
• Corresponding author

Nature Reviews Genetics

 

15,

 

49–55

 

(2014)

 

doi:10.1038/nrg3624

Published online

 

26 November 2013

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Abstract

• Abstract• 
• Introduction• 
• Genome sequencing in diagnostics• 
• The changing sequencing market•
• Bioinformatic challenges• 
• Regulations• 
• Future directions• 
• Accession codes• 
• References•
• Acknowledgements• 
• Author information• 
• Related links

The potential of bacterial whole-genome sequencing (WGS) to complement existing diagnostic infrastructures in clinical microbiology has been shown in proof-of-principle examples and extensively discussed. However, less attention has been drawn to bioinformatic challenges that are associated with the clinical adoption of WGS-based molecular diagnostics. This Perspective article discusses questions that are related to standard operating procedures, computational resource management, and data storage and integration in the context of recent developments in the sequencing and bioinformatics service markets.