CAMITAX

CAMITAX assigns taxonomic labels to microbial genomes from isolates, single cells, and metagenomes by integrating genome distance metrics, 16S ribosomal RNA gene analysis, gene homology comparisons, and phylogenetic placement into an ensemble classification framework.

Key Features:

• Ensemble classification: Combines genome distance metrics, 16S rRNA analysis, gene homology comparisons, and phylogenetic placement to produce consensus taxonomic assignments across ranks.
• Genome distance metrics: Applies genome distance-based comparisons for taxonomic inference of whole genomes.
• 16S rRNA gene analysis: Incorporates 16S ribosomal RNA gene-based classification for marker-gene evidence.
• Gene homology comparisons: Uses gene-level homology searches to inform taxonomic assignments.
• Phylogenetic placement: Employs phylogenetic placement strategies to refine taxonomic resolution.
• Workflow orchestration and reproducibility: Orchestrates reference databases and software containers with Nextflow to ensure computational reproducibility.
• Input scope: Designed to handle genomes derived from isolates, single-cell genomics, and metagenome assemblies.

Scientific Applications:

• Taxonomic labeling of microbial genomes: Assigns taxon labels to genomes at multiple taxonomic ranks using integrated evidence.
• Classification of metagenome-assembled genomes (MAGs): Applied to MAGs derived from metagenomic assemblies, including evaluation on TARA Oceans datasets.
• Method comparison and improvement: Provides an ensemble approach that improves accuracy relative to individual taxonomic assignment methods.

Methodology:

Integrates genome distance metrics, 16S rRNA gene analysis, gene homology comparisons, and phylogenetic placement into an ensemble classification framework; orchestrates reference databases and software containers with Nextflow; evaluated on several hundred metagenome-assembled genomes with high-quality taxonomic annotations from the TARA Oceans project.