In this report, we describe an algorithm, PanGenie (for Pangenome-based Genome Inference), that makes use of haplotype information from an assembly-derived pangenome representation in combination with readk-mer counts to efficiently genotype a wide spectrum of variants. That is, our method can l...
In the present study, we propose a new algorithm, PanGenie, that leverages a haplotype-resolved pangenome reference together with-mer counts from short-read sequencing data to genotype a wide spectrum of genetic variation鈥攁 process we refer to as genome inference. Compared with mapping-based ...
We performed phylogenetic and population structure analyses using 4,934,413 high-quality SNPs (minor allele frequencies ≥ 0.05 and missing genotype rates < 0.1; Fig.1a,band Supplementary Fig.2a). Based on population structure analysis, we classified the wild species into four subgroups—W...