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MAG Pipeline

Study pipeline · nf-core/mag v3.0.0

Metagenome assembly, binning, and QC in one workflow.

Study pipelinemetagenomicsnf-coreIlluminaNanoporeHybrid
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About

MAG is a production-ready workflow for assembling, binning, and evaluating metagenomes. It integrates QC, assembly, binning, taxonomy, and MultiQC reporting. Supports Illumina short reads, Oxford Nanopore long reads, and hybrid assembly.

Requirements

  • Nextflow 23.04+
  • Conda or Docker/Singularity
  • 16GB RAM minimum (64GB recommended)
  • GTDB database (optional, for taxonomy)

Workflow Notes

Metagenome assembly and binning using nf-core/mag with support for multiple assemblers (MEGAHIT, SPAdes) and binners (MetaBAT2, MaxBin2, CONCOCT) refined with DAS Tool.

Inputs

  • Paired-end FASTQ reads (Illumina)
  • Long reads (Nanopore, optional)
  • Samplesheet (auto-generated by SeqDesk)

Outputs

  • Assembled contigs (FASTA)
  • Genome bins / MAGs (FASTA)
  • Bin quality metrics (CheckM/BUSCO)
  • Taxonomic classification (GTDB-Tk)
  • MultiQC report (HTML)

MAG Pipeline Workflow

Data flow from declared study inputs through analysis steps to final outputs.