General-purpose embeddings for long-read metagenomic sequences via β-VAE on multi-scale k-mer frequencies

Long-read metagenomics routinely produces millions of assembled contigs, creating a need for methods that organize sequences into biologically meaningful groups across samples and environments. We present a general-purpose compositional embedding for metagenomic sequences based on a 𝛽-variational autoencoder (𝛽-VAE) trained on multi-scale k-mer frequencies (1-mers through 6-mers; 2,772 features with centered log- ratio transformation). The embedding compresses each contig into a 384-dimensional vector that preserves local compositional similarity, enabling similarity search and graph-based clustering from sequence composi- tion alone. Through systematic comparison of fifteen models trained on up to 17.4 million contigs (525.5 Gbp) from brackish, terrestrial, and reference genome sources, we find that a small set of curated prokaryotic refer- ence genomes (656,000 contigs) outperforms ten-fold larger domain-specific training sets, and that neither reconstruction loss nor Spearman correlation reliably predicts downstream clustering quality. On nearest- neighbor graphs, flow-based clustering (MCL) markedly outperforms modularity-based methods (Leiden), yielding 12,123 clusters from 154,041 contigs (≥ 100 kbp) with 99.2% phylum-level purity confirmed by inde- pendent marker gene phylogenetics. Multi-method taxonomic annotation achieves 87% coverage and reveals that 16.4% of contigs are eukaryotic - the single largest component invisible to standard prokaryotic anno- tation tools. The embedding provides a sample-independent coordinate system for organizing metagenomic sequence space at scale.