T2T-apes / ape_pangenome

pangenome analyses for complete genomes of great apes (and gibbon)

great ape pangenome analysis

All-to-all whole genome alignments and implicit pangenome graph model of a great ape pangenome. Writeup, this README is meant for working notes and links to repo elements.

overview

assemblies

See assemblies.

Alignment and chain files

See alignment.

Implicit pangenome graph

See impg.

wgatools pseudo-MAF

See wgatools.

Conservation analyses

See conservation.

Divergence

See divergence.

Incomplete lineage sorting (ILS)

See ils.