metamdbg

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  # if packaged; else follow upstream

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