Streamline unsupervised machine learning to survey and graph indel-based haplotypes from pan-genomes

Dear Editor,Pan-genomes with high quality de novo assemblies are shifting the paradigm of biology research in genome evolution,speciation,and function annotation(Shi et al.,2023).An all-vs.-all comparison across assemblies potentially overcomes the limitation of mapping short reads to a single assembly in cataloging polymorphisms,especially large insertions and deletions(indels)contributing to phenotypic variations through altering gene structure or expression(Chen et al.,2021).