Scripts and datasets in the study of archaic introgression in modern human genomes

Centromere diversity

Human Y chromosome evolution

Haplotype

Methods used in analysis in the PGA project

This repository for APG phase 1 contains scripts, workflows, and documentation for genome assembly, annotation, pangenome graph construction, SV/LoF analysis, and complex region characterization (MHC, SMN, centromeres, rDNA).

Assembly-based archaic introgression detector, a Hidden Markov Model that leverages haplotype-resolved human pangenome assemblies to detect complete archaic introgression sequences