Adaptive Tracepoints for Pangenome Alignment Compression

Data accompanying the manuscript "Adaptive Tracepoints for Pangenome Alignment Compression" (Kaushan, Marco-Sola, Garrison, Prins, Guarracino). This deposit contains: Simulated sequences: Random sequence pairs in FASTA format generated for combinations of sequence length (100 bp, 1 Kb, 10 Kb, 100 Kb) and divergence rate (1%, 5%, 10%, 20%), with N=10,000 pairs per condition. Simulated alignments: Alignments in TPA format of the simulated sequences. Real pangenome alignments: Human pangenome: 389M alignments in TPA format from 25,221 haplotype pairs sampled from HPRCv2 (466 haplotypes), generated with WFMASH. Primate pangenome: 566K alignments in TPA format from all-versus-all comparisons of 16 haplotypes across T2T ape genomes (Yoo et al., 2025), generated with WFMASH. Software: https://github.com/AndreaGuarracino/tracepoints, https://github.com/AndreaGuarracino/tpa, https://github.com/AndreaGuarracino/cigzip Analysis code: https://github.com/chris7716/tracepoints-paper