Haplotype-aware sequence alignment to pangenome graphs

G Chandra, D Gibney, C Jain - Genome Research, 2024‏ - genome.cshlp.org
Modern pangenome graphs are built using haplotype-resolved genome assemblies. When
map** reads to a pangenome graph, prioritizing alignments that are consistent with the …

Pangenome graph augmentation from unassembled long reads

L Denti, P Bonizzoni, B Brejova, R Chikhi, T Krannich… - bioRxiv, 2025‏ - biorxiv.org
Pangenomes are becoming increasingly popular data structures for genomics analyses due
to their ability to compactly represent the genetic diversity within populations. Constructing a …

RecAlign: A* recombination-aware sequence to graph map**

P Bonizzoni, DC Monti, G Della Vedova, B Riccardi… - bioRxiv, 2025‏ - biorxiv.org
Pangenomics and long reads bring the promise of integrating read map** with variant
calling, since a pangenome encodes a reference genome that incorporates evolutionary or …