| name | metabat2 |
| description | Adaptive contig binning from tetranucleotide composition and multi-sample coverage. Use for primary single-binner runs feeding DAS Tool, MetaWRAP, or BASALT ensembles. Upstream: https://bitbucket.org/berkeleylab/metabat.
|
| license | MIT |
| category | analysis-tools |
| tags | ["binning","metabat","coverage"] |
| upstream | https://bitbucket.org/berkeleylab/metabat |
| stage | binning |
MetaBAT 2
Upstream: berkeleylab/metabat
Citation
Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and
efficient genome reconstruction from metagenome assemblies. PeerJ 7,
e7359 (2019). https://doi.org/10.7717/peerj.7359
Analytical thinking
MetaBAT2 is the workhorse single binner. Quality hinges on depth from
sorted BAMs (jgi_summarize_bam_contig_depths) across samples that share the
assembly. One sample still works; multi-sample coverage usually improves
separation.
Treat MetaBAT2 bins as candidates — refine via dastool / metawrap /
basalt (recommended ensemble) and QC with checkm2.
Raise -m (min contig length) on huge assemblies to control runtime/noise;
document the threshold.
Prerequisites
| Requirement | Minimum | Recommended |
|---|
| Contigs | Assembly FASTA | |
| BAMs | Sorted+indexed | From bowtie2/strobealign/bwa-mem2 |
| Depth | jgi_summarize_bam_contig_depths | Same contig headers |
How to run
conda install -c bioconda metabat2 samtools
jgi_summarize_bam_contig_depths \
--outputDepth temp/map/depth.txt \
temp/map/*.bam
metabat2 -i contigs.fa -a temp/map/depth.txt \
-o temp/bins/metabat/bin \
-t 16 -m 1500 --seed 2024
Key parameters
| Option | Guidance |
|---|
-a | Depth table (required for multi-cov signal) |
-m | Min contig length (1500–2500 common) |
-t | Threads |
--seed | Reproducibility |
Outputs
temp/bins/metabat/bin.*.fa — feed to DAS Tool / CheckM2 / dRep.
Decision tree
Binning path?
├─ Only MetaBAT2 → ok for pilot; ensemble for catalogues
├─ Ensemble classical → metabat2 + maxbin2 (+ concoct) → dastool/metawrap
└─ Recommended related multi-assembly → basalt
Troubleshooting
| Symptom | Action |
|---|
| Empty bins | Depth contig IDs ≠ FASTA headers |
| Tiny bins only | Lower community signal / raise depth quality |
| RAM issues | Increase -m; run on high-mem node |
Related skills
bowtie2 · strobealign · samtools · maxbin2 · concoct · dastool · metawrap · basalt · checkm2
