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

Author

Listed:
  • 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
    Friedrich Schiller University)

  • F. A. Bastiaan Meijenfeldt

    (Utrecht University
    NIOZ Royal Netherlands Institute for Sea Research)

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.

Suggested Citation

  • Ernestina Hauptfeld & Nikolaos Pappas & Sandra Iwaarden & Basten L. Snoek & Andrea Aldas-Vargas & Bas E. Dutilh & F. A. Bastiaan Meijenfeldt, 2024. "Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47155-1
    DOI: 10.1038/s41467-024-47155-1
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