Benchmarking shotgun metagenomics

Nature Microbiology, Published online: 24 April 2026; doi:10.1038/s41564-026-02344-0 Shotgun metagenomic sequencing is a comprehensive untargeted next-generation sequencing method that enables culture-independent analysis of complex microbial communities. Comparing the results of several metagenome-based analyses at various sequencing depths for known input illustrates which methods and amounts of data are most suitable for determining microbial composition, accuracy of metagenome-assembled geno