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MAG Pipeline

nf-core/mag v3.0.0

Metagenome assembly, binning, and QC in one workflow.

Metagenomicsnf-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.

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)

Outputs

  • Assembled contigs (FASTA)
  • Genome bins / MAGs (FASTA)
  • Bin quality metrics
  • Taxonomic classification
  • MultiQC report

MAG Pipeline Workflow

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