omics.co.in

Chapter 11: Metagenome-Assembled Genomes (MAGs): Binning with MetaBAT2 & MaxBin

1 min read • Updated Oct 2026 • Peer-Reviewed Learning Resource

Chapter 11: Metagenome-Assembled Genomes (MAGs): Binning with MetaBAT2 & MaxBin

Assembling a metagenome produces tens of thousands of fragmented contigs. Metagenomic binning clusters these contigs into discrete organismal genomes, generating Metagenome-Assembled Genomes (MAGs) representing uncultured novel bacterial and archaeal species.

The Two Biological Signals for Binning
  • Tetranucleotide Frequency (TNF): The 4-mer genomic composition reflects species-specific DNA replication and repair machinery biases. Contigs from the same organism share identical TNF signatures.
  • Differential Coverage (Co-abundance): Across multiple biological samples, contigs originating from the same physical bacterial cell must rise and fall in sequencing depth in lockstep.

1. Binning Workflow with MetaBAT2

# 1. Map reads from all cohort samples against the assembled contigs
bwa-mem2 mem -t 16 contigs.fasta sample1_R1.fq.gz sample1_R2.fq.gz | samtools sort -o sample1.bam -

# 2. Calculate co-abundance depth matrix across all BAM files
jgi_summarize_bam_contig_depths --outputDepth depth.txt sample*.bam

# 3. Bin contigs with MetaBAT2
metabat2 -i contigs.fasta -a depth.txt -o ./bins/bin -m 1500 --seed 42

2. Consensus Bin Refinement with DAS Tool

Running multiple distinct binning algorithms (MetaBAT2, MaxBin2, CONCOCT) and combining them with DAS Tool (Dereplication, Aggregation and Scoring) recovers 30–50% more high-quality MAGs than any single tool alone.

← Return to Home Hub Scroll to Top ↑