EukBin is a specialized binning tool for eukaryotic metagenomes that combines repeat-masked tetranucleotide frequency (TNF), multi-sample coverage information, BUSCO marker gene constraints, and deep learning (β-VAE with contrastive loss) with ploidy-aware refinement.

Key features: - Repeat-masked TNF features to handle repeat-rich eukaryotic genomes - BUSCO-guided constraints for accurate bin estimation - Ploidy-aware refinement (haplotig detection for diploid/polyploid genomes) - Deep learning with β-VAE and contrastive loss - Supports multi-sample binning

This package includes: - eukbin run: Complete binning pipeline (M1-M6 modules) - eukbin evaluate: Quality assessment for any binning tool - eukbin report: Multi-tool comparison report

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