A user's guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection

2023/11/16 by Blake G. Lindner, Kenji Gerhardt, K. Gerhardt +5 · 2 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Bacteriophages and microbial interactions #Genomics and Phylogenetic Studies #Microbial Community Ecology and Physiology

paper · doi:10.1016/j.ijfoodmicro.2023.110488

openalex publication_date 2023/11/16 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01

Citations

• Accurate and complete genomes from metagenomes
• Analysis of compositions of microbiomes with bias correction
• Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
• Bioetica - clonazione - tutela persona e della vita
• Towards estimating the number of strains that make up a natural bacterial population

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• An ANIr-based methodology to determine if two sequence-discrete populations are identical and identify cosmopolitan prokaryotic populations
• Portable metagenomics for preventive surveillance and outbreak control in livestock and poultry: Pathogen detection, resistome profiling, and antimicrobial stewardship