Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes

Ernestina Hauptfeld, Nikolaos Pappas, Sandra Iwaarden, Basten L. Snoek, Andrea Aldas-Vargas, Bas E. Dutilh () and F. A. Bastiaan Meijenfeldt ()
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Ernestina Hauptfeld: Utrecht University
Nikolaos Pappas: Utrecht University
Sandra Iwaarden: Utrecht University
Basten L. Snoek: Utrecht University
Andrea Aldas-Vargas: Wageningen University & Research
Bas E. Dutilh: Utrecht University
F. A. Bastiaan Meijenfeldt: Utrecht University

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.

Date: 2024
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DOI: 10.1038/s41467-024-47155-1

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