MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies

Trine Zachariasen (), Jakob Russel, Charisse Petersen, Gisle A. Vestergaard, Shiraz Shah, Pablo Atienza Lopez, Moschoula Passali, Stuart E. Turvey, Søren J. Sørensen, Ole Lund, Jakob Stokholm, Asker Brejnrod and Jonathan Thorsen
Additional contact information
Trine Zachariasen: Technical University of Denmark
Jakob Russel: University of Copenhagen
Charisse Petersen: 950 West 28th Avenue
Gisle A. Vestergaard: Technical University of Denmark
Shiraz Shah: University of Copenhagen
Pablo Atienza Lopez: Rigshospitalet-Glostrup
Moschoula Passali: Rigshospitalet-Glostrup
Stuart E. Turvey: 950 West 28th Avenue
Søren J. Sørensen: University of Copenhagen
Ole Lund: Technical University of Denmark
Jakob Stokholm: University of Copenhagen
Asker Brejnrod: Technical University of Denmark
Jonathan Thorsen: University of Copenhagen

Nature Communications, 2024, vol. 15, issue 1, 1-10

Abstract: Abstract Metagenomic sequencing has provided great advantages in the characterisation of microbiomes, but currently available analysis tools lack the ability to combine subspecies-level taxonomic resolution and accurate abundance estimation with functional profiling of assembled genomes. To define the microbiome and its associations with human health, improved tools are needed to enable comprehensive understanding of the microbial composition and elucidation of the phylogenetic and functional relationships between the microbes. Here, we present MAGinator, a freely available tool, tailored for profiling of shotgun metagenomics datasets. MAGinator provides de novo identification of subspecies-level microbes and accurate abundance estimates of metagenome-assembled genomes (MAGs). MAGinator utilises the information from both gene- and contig-based methods yielding insight into both taxonomic profiles and the origin of genes and genetic content, used for inference of functional content of each sample by host organism. Additionally, MAGinator facilitates the reconstruction of phylogenetic relationships between the MAGs, providing a framework to identify clade-level differences.

Date: 2024
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DOI: 10.1038/s41467-024-49958-8

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