MetaPhage

MetaPhage performs automated analysis, annotation, and classification of bacteriophages from metagenomic sequencing datasets to characterize phage diversity and roles in microbial communities.

Key Features:

• Comprehensive Pipeline: Integrates multiple phage mining strategies into a unified workflow that processes raw sequencing reads through to summary reports.
• Report Generation: Produces detailed reports with visualizations and summary tables aggregating phage identification, annotation, and classification results.
• Scalability and Reproducibility: Implemented in Nextflow to enable task parallelization across computing environments and reproducible execution via containerized packages.
• Extensibility: Modular architecture permits incorporation of additional phage miners and analytical methodologies.

Scientific Applications:

• Environmental Phage Ecology: Identification and characterization of bacteriophages in environmental metagenomes such as oceans and soils.
• Human Microbiome Studies: Profiling phages in human microbiota to investigate phage–bacterial interactions and horizontal gene transfer.
• Microbial Community Dynamics: Assessing phage contributions to bacterial community structure, predation, and ecosystem functions.

Methodology:

The pipeline is implemented in Nextflow and integrates multiple phage-mining strategies, enabling parallelized execution and reproducibility via containerized packages while processing raw sequencing reads to generate annotated and classified phage reports.