nf-core mag

nf-core mag performs assembly, binning, annotation, and taxonomic profiling of shotgun metagenomic sequencing reads to reconstruct metagenome-assembled genomes (MAGs) and characterize microbial community composition.

Key Features:

• Integration of Short and Long Reads: Optionally combines short- and long-read sequencing data to improve assembly continuity and genome reconstruction.
• Co-assembly and Genome Binning: Supports sample-wise co-assembly and genome binning using group information to leverage multiple samples for improved MAG recovery.
• Taxonomic Classification: Performs taxonomic classification of assembled genomes or bins to characterize microbial community composition.
• Reproducibility and Portability: Implemented in Nextflow with containerized dependencies to ensure reproducible, portable execution across computational environments.

Scientific Applications:

• Genome-resolved Metagenomics: Reconstruction of MAGs from complex microbial communities for downstream genomic and functional analyses.
• Microbial Ecology and Environmental Microbiology: Profiling microbial diversity, function, and interactions in microbiology, ecology, and environmental science using genome-resolved data.

Methodology:

Data preprocessing; assembly (optionally integrating short and long reads) and co-assembly; sample-wise genome binning; genome annotation; and taxonomic classification.