great ape pangenome analysis

April 14, 2024 ยท View on GitHub

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.

Contents

  1. 1overview
  2. 1.1assemblies
  3. 1.2Alignment and chain files
  4. 1.3Implicit pangenome graph
  5. 1.4wgatools pseudo-MAF
  6. 1.5Conservation analyses
  7. 1.6Divergence
  8. 1.7Incomplete lineage sorting (ILS)