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pangenome-analysis

separate

Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.

When to use

• assembling species- or genus-level pan-gene catalogs
• separating core from accessory/shell/cloud genes
• testing gene-content associations with phenotypes
• building pangenome graphs from haplotype-resolved assemblies
• calling SVs from pangenome graphs
• selecting between bacterial-pangenome and eukaryotic-pangenome workflows

When not to use

• Roary-based analysis

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