| name | metamdbg |
| description | High-quality metagenome assembly from long accurate reads. Use this skill when working with metamdbg: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/GaetanBenoitDev/metaMDBG. For stage routing use tool-selection / metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["assembly","hifi","long-read"] |
| upstream | https://github.com/GaetanBenoitDev/metaMDBG |
| stage | assembly |
metaMDBG
Upstream: metaMDBG
Citation
Benoit, G. et al. High-quality metagenome assembly from long accurate reads with metaMDBG. Nat. Biotechnol. 42, 1378–1383 (2024). https://doi.org/10.1038/s41587-023-01983-6
See also docs/references.md.
Analytical thinking
Preferred for PacBio HiFi / accurate long-read metagenomes. Pair with long-read-aware binning (SemiBin2/LorBin/BASALT).
How to run
conda install -c bioconda metamdbg
metaMDBG asm --out temp/asm/metamdbg --in reads.fastq.gz --threads 32
Key parameters
| accurate long reads | HiFi/duplex | |
| check upstream CLI | version-sensitive | |
Decision notes
- Stage: assembly (long accurate reads)
- Prefer HiFi / accurate long reads; follow with long-read binning (
lorbin / SemiBin2 LR)
- Pin version; report polish status
Related skills
metaflye · minimap2 · semibin2 · basalt · tool-selection · metagenomics-workflow
