aamb

name	aamb
description	AAMB / AVAMB — adversarial autoencoder metagenomic binning and its ensemble with VAMB for improved near-complete MAG recovery. Use when: (1) Running AAMB as a DL single binner, (2) AVAMB ensemble (VAMB+AAMB) for extra NC genomes, (3) Diversifying bins before DAS Tool/BASALT. Upstream (VAMB tree): https://github.com/RasmussenLab/vamb. Still QC with checkm2; prefer basalt ★ for multi-assembly catalogues.
license	MIT
category	analysis-tools
tags	["binning","AAMB","AVAMB","VAMB","deep-learning"]
upstream	https://github.com/RasmussenLab/vamb
stage	binning

AAMB / AVAMB

Upstream: RasmussenLab/vamb (AAMB/AVAMB paths documented in the VAMB repository)

Citation

Piera Líndez, P. et al. Adversarial and variational autoencoders improve metagenomic binning. Commun. Biol. 6, 1073 (2023). https://doi.org/10.1038/s42003-023-05452-3

See also docs/references.md.

Analytical thinking

AAMB uses adversarial autoencoders on coabundance + TNF; AVAMB ensembles AAMB with VAMB and recovered substantially more near-complete genomes in the paper vs VAMB alone. Treat as a diverse DL binner for ensembles — not a replacement for basalt multi-assembly refinement.

Related VAMB-family tools: vamb, taxvamb.

How to run

# see VAMB docs for aamb / avamb entry points for your installed version
# typical: provide contigs + BAM abundance as with VAMB

Related skills

vamb · taxvamb · semibin2 · dastool · basalt · tool-selection