PopMAG
PopMAG is a pipeline that integrates genome-resolved metagenomics with population genomics tools to analyze metagenome-assembled genomes (MAGs) and their population-level variations. The pipeline processes MAGs alongside paired-end sequencing short reads (or BAM files) to perform quality assessment, abundance profiling, variant calling, and population genomics analyses, ending in an interactive visualization dashboard built with shiny.
The pipeline is organized into five main phases:
MAG Quality control and preprocessing
Microbial community profiling
Abundance calculation and variant calling
Population genomics and functional analysis
Visualization and reporting
PopMAG can aid to understand both the functional potential and population dynamics of metagenome-assembled genomes, particularly in the context of comparative genomics and temporal or spatial studies.
Check out the Usage section for further information, including how to install the project.
Note
This project is under active development.