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High-quality phage assembly from metagenomes with PALACE
Ruo Han Wang1, Guangze Pan1, Shuai Wang1
1Department of Computer Science, City University of Hong Kong, Hong Kong, China.
Nature Biotechnology
|July 9, 2026
Summary
PALACE, a new framework, significantly improves phage genome assembly from metagenomic data. It yields more complete and accurate phage genomes, especially in complex gut environments like colorectal cancer (CRC).
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Metagenomic data mining has revealed millions of phage genomes, but poor genome completeness hinders research.
- Existing phage detection methods fragment phage genomes due to reliance on metagenomic contigs.
Purpose of the Study:
- To develop a novel framework, PALACE, for assembling high-quality phage genomes from metagenomic data.
- To improve the accuracy and completeness of phage genome reconstruction.
Main Methods:
- PALACE utilizes a conjugate-graph-based framework incorporating homology-based and deep-learning methods.
- It constructs a conjugate graph from metagenomic samples to assemble phage genomes.
Main Results:
- PALACE achieved high accuracy and completeness on simulated data, with F1 scores of 0.92-1.00.
- Applied to human gut metagenomes, PALACE yielded 5,306 high-quality phage genomes, significantly improving median genome completeness by 55.98% compared to benchmark methods.
- Phages from colorectal cancer (CRC) patients showed enriched metabolic factors, suggesting adaptation to the CRC gut environment.
Conclusions:
- PALACE is an effective framework for assembling high-quality phage genomes from metagenomic data.
- The findings suggest phages may adapt to the CRC gut environment by altering their metabolic functions.
