Puccinia graminis f. sp. tritici (Pgt) PacBio genome sequencing project Scripts for the paper: Li et al., Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation. Nature Communications. Pgt isolates: Ug99 and 21-0 de novo haplotype-phased genome assembly of stem rust fungus: use canu assembler genome annotation: use funannotate variant calling and genome coverage analysis: freebayes and samtools variant calling