How does tandem repeat TR map to the PGGB-constructed pan-genome

[dong1yang]

Hello, may I ask a question? I have 200 haplotype genomes, and I conduct tandem repeat TR sequence identification for each genome from scratch. Using PN40024 genome as the skeleton, a pan-genome of 200 genomes was constructed using PGGB method. The identified TR sequences in each genome have their own location information. How to map the identified TR sequences of different genomes to the pan-genome? The TR sequence has the following characteristics: 1. The TRS identified in each genome are different, for example, 5,000 TRS are identified in the reference genome, while 6,000 TRS are identified in a certain sample genome. 2. Tandem repeats of TR may be the same at different locations in a genome, such as an ACC motif repeated 10 times on chr1 1000-1030 and 5 times on chr1 2050-2065. It is also possible that the TR is absent from other genomic alignments. Based on the above characteristics. How do we map TR onto the pan-genome to form a Pan-TR variation file, and is there any good way for PGGB to do this in terms of mapping?