3CAC

3CAC classifies sequence contigs from mixed metagenomic assemblies into phages, plasmids, and bacterial chromosomes to improve identification of mobile genetic elements and host chromosomes.

Key Features:

• Three-class classification: Distinguishes contigs into phages, plasmids, and bacterial chromosomes.
• Initial classifier integration: Leverages preliminary classifications from viralVerify, PPR-Meta, PlasClass, and deepVirFinder.
• Assembly graph proximity refinement: Uses assembly graph proximity to refine initial contig classifications.
• Improved short/low-confidence contig handling: Targets improved accuracy for short contigs and contigs with low confidence scores.
• Performance gains: Increases precision, recall, and F1-score compared to PPR-Meta and viralVerify, with F1-score improvements of 10-60 percentage points.
• Benchmarking: Evaluated on simulated metagenomes and real human gut microbiome samples.

Scientific Applications:

• Mobile genetic element identification: Separation and identification of bacteriophages and plasmids within metagenomic assemblies.
• Microbial evolution studies: Elucidation of roles of bacteriophages and plasmids within their host bacteria.
• Metagenomic assembly analysis: Improved contig-level classification in mixed metagenomic assemblies, including cases with high chromosome contig fractions.
• Downstream genomics and microbiology research: Enables analyses that require accurate distinction between phage, plasmid, and chromosomal sequences.

Methodology:

Uses preliminary classifications from viralVerify, PPR-Meta, PlasClass, and deepVirFinder and refines them using assembly graph proximity to reclassify contigs, with emphasis on improving short contigs and low-confidence predictions.