Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

By H. B. Nielsen, Mathieu Almeida, Agnieszka Sierakowska Juncker, S. Rasmussen, Junhua Li, Shinichi Sunagawa, D. Plichta, L. Gautier, A. G. Pedersen, E. Le Chatelier and 82 more. 2014

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Extensive impact of non-antibiotic drugs on human gut bacteria (2018, neutral): “To select a representative core of species in the human gut microbiome, we analyzed 364 fecal metagenomes of asymptomatic individuals from 3 continents 44–47.”
MGnify: the microbiome sequence data analysis resource in 2023 (2022, background): “Approaches for the recovery of genomes from environmental samples first appeared in 2004 (5), with reference-free approaches being developed in the following decade (6).”
Probiotics, gut microbiota, and their influence on host health and disease (2017, methodology): “Genes are clustered based on their abundance data using the Canopy-based algorithm and the profiles of these groups may be calculated as the samplewise median gene abundance [116].”
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle (2019, background): “Draft genomes include also metagenomic species that are explicitly labeled with the ‘‘MAG’’ abbreviation (n = 37) and co-abundance gene groups metagenomic assemblies (CAGs, n = 377) (Nielsen et al., 2014).”
A review of methods and databases for metagenomic classification and assembly (2019, background): “MGS Canopy [135] generates abundance profiles of gene calls and clusters them by co-abundance across samples.”