Intro

TelomereHunter2 detects telomeric and telomere-adjacent reads in genome sequencing data and summarizes telomere content as a normalized metric. It also reports telomeric variant repeat (TVR) composition.

Inputs

• BAM/CRAM: aligned sequencing reads
• Cytoband file (-b): used to determine the first/last band per chromosome (subtelomeric context)
• Sample / pair ID (-p): identifier used for file names and report labels

Bulk vs single-cell

• Bulk (telomerehunter2): processes one BAM/CRAM (optionally tumor+control) and generates summary tables and plots.
• Single-cell (telomerehunter2-sc): processes a BAM with barcode tags and reports per-cell metrics.

Outputs (high level)

• *_summary.tsv: telomere content and read category counts
• *_TVR_top_contexts.tsv: top TVR contexts
• *_singletons.tsv: singleton TVR statistics
• plots/ and html_reports/: figures and HTML reports (if enabled)