Skill: metagenome-binning

Use When

• The user wants to recover individual microbial genomes from assembled metagenomic contigs.
• The user needs MAG quality assessment (completeness, contamination).
• The user wants to refine bins from multiple binners with DAS Tool.
• The user needs MIMAG-standard quality classifications for recovered genomes.

Inputs

• Required:
  • Assembled contigs FASTA file.
  • BAM file of reads mapped back to contigs (for coverage calculation).
• Optional:
  • --das-tool — Enable DAS Tool refinement using multiple binner results.
  • --min-contig N — Minimum contig length for binning in bp (default: 1500).
  • --threads N — Number of threads (default: 4).
  • --outdir DIR — Output directory (default: binning_results).
  • --checkm2-db PATH — Path to CheckM2 database.

Workflow

1. Calculate contig coverage depth with MetaBAT2's jgi_summarize_bam_contig_depths.
2. Run MetaBAT2 for initial binning.
3. Optionally run additional binners (MaxBin2, CONCOCT) for DAS Tool refinement.
4. If multiple binners used: run DAS Tool to select the best non-redundant bin set.
5. Run CheckM2 predict on the final bin set for completeness and contamination estimates.
6. Classify bins by MIMAG standards: high-quality (>=90% complete, <5% contamination), medium-quality (>=50%, <10%), low-quality (below thresholds).
7. Report: number of bins, quality distribution, total high/medium/low quality MAGs.

Output Contract

• MAG FASTA files — One FASTA file per bin (<outdir>/bins/<bin_id>.fa).
• CheckM2 quality report — Completeness and contamination per bin (<outdir>/checkm2/quality_report.tsv).
• Bin quality summary — Per-bin completeness, contamination, N50, genome size, and MIMAG classification (<outdir>/bin_summary.txt).

Limits

• MetaBAT2 and CheckM2 must be installed and available on $PATH.
• CheckM2 requires a pre-downloaded database (approximately 3 GB).
• DAS Tool requires results from multiple binners as input; it is optional but recommended.
• Assembly must have sufficient depth for binning (>10x per genome is recommended).
• Contigs shorter than 1500 bp are typically excluded from binning.
• MIMAG quality standards: high-quality draft (>=90% completeness, <5% contamination), medium-quality draft (>=50% completeness, <10% contamination).
• Common failure cases:
  • BAM file not sorted or indexed, causing jgi_summarize_bam_contig_depths to fail.
  • CheckM2 database not downloaded or path not set, preventing quality assessment.
  • Insufficient sequencing depth (<10x per genome) producing fragmented or empty bins.