High-quality phage assembly from metagenomes with PALACE.

PALACE achieves near-perfect assembly of 5,306 high-quality phage genomes from gut metagenomes, with median completeness surpassing previous methods by nearly 56%.

• Why it matters: Accurate and complete phage genomes are crucial for understanding their roles in human health and disease, but existing methods fragment genomes, limiting insights.
• What they did: The study developed PALACE, a conjugate-graph-based framework combining homology and deep learning to detect phage signals and assemble genomes from 914 gut samples, achieving an F1 score of up to 1.00 in simulations.
• The result: PALACE outperformed existing tools significantly, enabling detailed functional and ecological analyses, such as identifying metabolic gene enrichment in phages from colorectal cancer patients, advancing microbiome research.