TAREAN

TAREAN identifies satellite repeats directly from unassembled sequence reads using graph-based clustering of low-pass whole genome sequencing data to characterize satellite DNA.

Key Features:

• Unsupervised repeat identification: Performs unsupervised identification of satellite repeats from unassembled sequencing reads.
• Low-pass WGS input without assembly: Operates on low-pass whole genome sequencing data and does not require genome assembly.
• Graph-based sequence clustering: Employs graph-based clustering to group reads representing repetitive elements.
• Circular cluster detection: Detects putative satellite repeats by identifying characteristic circular structures within cluster graphs.
• Consensus monomer reconstruction from k-mers: Reconstructs consensus sequences of repeat monomers from the most frequent k-mers obtained by decomposing reads within identified clusters.
• Targeting tandem arrays: Specifically addresses tandemly arranged repeat copies that form extensive contiguous arrays spanning large genomic regions.

Scientific Applications:

• Satellite DNA characterization: Identification and characterization of satellite DNA in complex genomes directly from unassembled reads.
• Novel satellite discovery: Prediction of novel satellite repeats, exemplified by discoveries in Vicia faba with three repeats experimentally verified by fluorescence in situ hybridization (FISH) on metaphase chromosomes.
• Validation and benchmarking: Validation using low-pass genome sequencing data from five plant species with previously characterized satellite DNA.

Methodology:

Uses low-pass whole genome sequencing reads without assembly; applies graph-based sequence clustering to identify repeat-containing clusters and detect circular cluster graph structures indicative of satellites; decomposes reads into k-mers and reconstructs consensus repeat monomers from the most frequent k-mers within clusters.