Scripts utilized for the graph-based pan-genome analysis of cotton

Document description

• 01_Genome assembly Genome assembly analysis
• 02_PAV calling PVA calling process
• 03_SNP calling SNP calling process
• 04_GO Annotation GO annotation analysis
• 05_Introgression block analysis Introgression block analysis
• 06_Full-length LTR identification Full-length LTR identification
• 07_Pan-genome construction Pan-genome construction
• 08_RNA-seq analysis Gene expression and PAV-eQTL analysis
• 09_GWAS PAV based GWAS analysis

---

Pipeline for PAV calling

Pipeline for pan-genome comparison