| name | maxbin2 |
| description | Automated multi-metagenome contig binning. Use this skill when working with maxbin2: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://sourceforge.net/projects/maxbin2/. For stage routing use tool-selection / metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["binning","maxbin"] |
| upstream | https://sourceforge.net/projects/maxbin2/ |
| stage | binning |
MaxBin 2
Upstream: MaxBin 2
Citation
Wu, Y.-W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605–607 (2016). https://doi.org/10.1093/bioinformatics/btv638
See also docs/references.md.
Analytical thinking
MaxBin 2 uses nucleotide composition + differential abundance across samples
(expectation-maximization). It is a classical workhorse and a valuable
ensemble member because it often recovers different genomes than MetaBAT2.
| vs MetaBAT2 | Notes |
|---|
| Strength | Multi-sample abundance model; widely packaged in MetaWRAP |
| Weakness | Slower / heavier on huge contig sets; fewer adaptive TNF tricks |
Prefer multi-coverage abundance tables. Always QC with CheckM2; for catalogues
feed into basalt ★ / metawrap / dastool.
How to run
run_MaxBin.pl -contig contigs.fa -abund depth.txt \
-out temp/bins/maxbin -thread 16
Key parameters
| Flag | Notes |
|---|
-abund | Coverage table(s); IDs must match contig headers |
-thread | Threads |
| min contig length | Follow upstream defaults or justify |
Decision tree
Single classical binner?
├─ Adaptive TNF+coverage → metabat2
├─ EM abundance+composition → maxbin2
├─ GMM composition+coverage → concoct
└─ Catalogue / multi-assembly → basalt ★
Related skills
metabat2 · concoct · dastool · metawrap · basalt · checkm2 ·
tool-selection
