CAMITAX: Taxon labels for microbial genomes

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• The exponential growth of microbial genome sequences necessitates reliable taxonomic labeling for downstream analyses.
• Advances in metagenomics and single-cell sequencing yield more complete microbial genomes, increasing the need for accurate classification.

Purpose of the Study:

• To introduce CAMITAX, a scalable and reproducible workflow for taxonomic labeling of microbial genomes.
• To provide a comprehensive software package for assigning taxon labels to microbial genomes from isolates, single cells, and metagenomes.

Main Methods:

• CAMITAX integrates multiple taxonomic assignment strategies: genome distance, 16S ribosomal RNA gene analysis, and gene homology.
• Phylogenetic placement is combined with other methods for robust taxonomic assignment.
• The workflow utilizes Nextflow for orchestrating reference databases and software containers, ensuring ease of use and computational reproducibility.

Main Results:

• CAMITAX was evaluated on hundreds of metagenome-assembled genomes from the TARA Oceans project.
• The ensemble classification method within CAMITAX demonstrated improved accuracy across tested taxonomic ranks compared to individual methods.
• The workflow proved effective for taxonomic labeling of microbial genomes from diverse sources.

Conclusions:

• CAMITAX evolved from the Critical Assessment of Metagenome Interpretation (CAMI) initiative into a comprehensive tool.
• The software package reliably assigns taxon labels to microbial genomes, aiding research in microbiology and metagenomics.
• CAMITAX is available as an open-source software package under the Apache License 2.0.