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MAGGIC

MAGGIC (Metagenomically Assembled Genome Generation with Integrated Classification) is an automated workflow for the generation and refinement of Metagenome-Assembled Genomes (MAGs) from metagenomic sequencing data.

It integrates multiple binning algorithms (VAMB, SemiBin2, MetaBat 2) followed by consensus-based bin refinement with Binette, taxonomic classification with GTDB-Tk, mobile genetic element detection with geNomad, and antimicrobial resistance gene profiling with AMRFinderPlus.

MAGGIC supports both short-read (--pipeline maggic) and long-read (--pipeline maggic_lr) metagenomic sequencing data.

Contents

• 1. Installation Requirements
• 2. Database Requirements
• 3. Usage Examples
  • 3.1. Multi-Sample Binning
  • 3.2. CLI Reference
• 4. Results Overview
  • 4.1. Bin Classification
  • 4.2. Plasmid & Virus Metrics
  • 4.3. AMR Profiling
  • 4.4. MAGGIC Plots
• 5. Future Roadmap

Future Roadmap

• 06/04/2026: Will address BAM low depth issues in later versions. <1% mapped && <100K reads && <5000 contigs will be filtered out.