TRASH

TRASH annotates tandem repeats and maps their higher-order structure in assembled nucleotide sequences from long-read DNA sequencing assemblies to enable de novo analysis of megabase-scale satellite repeat arrays, including eukaryotic centromeres.

Key Features:

• De novo repeat identification: Operates without prior knowledge of repeat composition or monomer sequences to detect tandem repeats.
• Input format: Analyzes fasta assembly files from assembled genomes.
• Tandem repeat mapping: Pinpoints regions occupied by tandem repeats within nucleotide assemblies.
• Higher-order structure detection: Identifies and maps patterns of higher-order repetition within repeat arrays.
• Satellite and centromere targeting: Detects megabase-scale satellite repeat arrays characteristic of eukaryotic centromeres.
• Long-read assembly compatibility: Designed for use with assemblies enabled by long-read DNA sequencing technologies.
• Scalability: Applicable to large and diverse genomic datasets, including plant and human assemblies.

Scientific Applications:

• Centromere research: Analysis of centromeric satellite arrays, demonstrated on the Col-CEN genome of Arabidopsis thaliana and the human CHM13 genome.
• Satellite repeat characterization: Detailed annotation of megabase-scale satellite repeat arrays and their organizational hierarchy.
• Cross-genome repeat analysis: Comparative analysis of tandem repeat structure across diverse genomic assemblies.

Methodology:

Analyzes fasta assembly files to identify regions occupied by tandem repeats and to map repeats and their higher-order structures, operating de novo without requiring prior knowledge of monomer sequences.