Bioinformatic pipeline for profiling foodborne bacterial ecology and resistome from short-read metagenomics - Archive ouverte HAL
Chapitre D'ouvrage Année : 2024

Bioinformatic pipeline for profiling foodborne bacterial ecology and resistome from short-read metagenomics

Résumé

Next generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.
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hal-04695572 , version 1 (12-09-2024)

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  • HAL Id : hal-04695572 , version 1

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Arnaud Bridier, Pierre Lemée. Bioinformatic pipeline for profiling foodborne bacterial ecology and resistome from short-read metagenomics. Foodborne Bacterial pathogens-2nd edition, In press. ⟨hal-04695572⟩

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