TideCluster: clustering and classification of tandem repeats for comparative and pangenomic analysis

TideCluster builds genome-wide, interpretable satellite DNA repeat family catalogs by clustering tandem repeat arrays and reconstructing monomer consensus, including locus periodicity and higher-order repeats.

• Why it matters: Satellite DNA is important in plant and animal genomes, but comparative analyses across arrays, chromosomes, and genomes are hard because structured, reference-independent tools are missing.
• What they did: The pipeline takes a genome assembly, consolidates fragmented tandem repeat detections into arrays, clusters arrays by sequence similarity, reconstructs monomer consensus, estimates locus-specific periodicity, identifies higher-order repeats, and outputs GFF3 annotations.
• The result: Applied to Arabidopsis thaliana and multiple Solanum species, it handles highly diverse satellite complements with monomer lengths from a few base pairs to more than 20 kb, enabling comparative and pangenomic analyses.

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