Fig. 1.

TelomereHunter workflow. a TelomereHunter extracts reads containing telomere repeats from an input BAM file. The reads are sorted by mapping position into intrachromosomal, subtelomeric, junction spanning and intratelomeric reads. From the intratelomeric reads, telomere content, telomere variant repeats and singletons are obtained. b Examples of a typical intratelomeric read containing a TGAGGG singleton and a typical subtelomeric read containing multiple telomere variant repeats in arbitrary context