Hoiho

This repo contains scripts and working directories for Hoiho (yellow-eyed penguin) genomics analyses.

Authors: Joseph Guhlin^1,2, Jordan Douglas^3,4

Repository layout

Core pipeline workspaces

• 00_Genome_Assembly/ — genome assembly workspace (currently empty placeholder).
• 01_Genome_Annotation/ — genome annotation workspace (currently empty placeholder).
• 02_Variant_Calling/ — variant calling workspace (currently empty placeholder).
• 03_Variant_Filtering/ — variant filtering workspace (currently empty placeholder).

Analysis workspaces

• ANALYSIS_aDNA_Variant_Calling/ — ancient DNA variant calling analysis workspace (currently empty placeholder).
• ANALYSIS_Ancestral_Recombination_Graphs/ — ARG analyses workspace (currently empty placeholder).
• ANALYSIS_Genome_Wide_Association_Studies/ — GWAS analyses workspace (currently empty placeholder).
• ANALYSIS_Imputation_and_Phasing/ — imputation/phasing analyses workspace (currently empty placeholder).
• ANALYSIS_Migration/ — migration analyses workspace (currently empty placeholder).
• ANALYSIS_Phylogenetics_BEAST/ — BEAST phylogenetics analyses workspace (currently empty placeholder).
• ANALYSIS_Population_Genomic_Statistics/ — population genomics statistics workspace (currently empty placeholder).
• ANALYSIS_Whole_Genome_Alignment_Seabirds/ — seabird WGA workspace (currently empty placeholder).

Scripts and notebooks

• scripts/ — analysis scripts, notebooks, and small utilities.
  • scripts/general/ — exploratory notebooks and helpers (PCA, heterozygosity, sex chromosome analyses; .ipynb, .sh, .bash, .qmd, pixi.toml).
  • scripts/gwas/ — phenotype processing + GWAS/TASSEL runners (.ipynb, .sh, .py).
  • scripts/phylogenetics_beast/ — building sequences/SNP inputs for BEAST + utilities (.ipynb, .py, .sh).
    • scripts/phylogenetics_beast/tools/ — small FASTA/region stats helpers (.py).
    • scripts/phylogenetics_beast/adna/ — aDNA-specific helpers (currently just subfolders).
      • scripts/phylogenetics_beast/adna/richdalei/ — richdalei aDNA calling/error estimation/rescue scripts (.py, .sh).
      • scripts/phylogenetics_beast/adna/waitaha/ — waitaha aDNA calling/error estimation scripts (.py, .sh).
  • scripts/migration/ — migration model runs + trace inspection (.sh, .ipynb, pixi.toml).
  • scripts/arg/ — ARG sampling/filtering helpers (.sh, .py, pixi.toml).
  • scripts/circos/ — Circos track generation notebooks + config (.ipynb, circos.conf).
  • scripts/population_genomics/ — local PCA notebook + environment (.ipynb, pixi.toml).
  • scripts/variant_filtering/ — standardized filtering run scripts (.sh).
  • scripts/adna/ — reserved for aDNA scripts (currently empty placeholder).
  • scripts/wga/ — whole-genome alignment helpers and utilities.
    • scripts/wga/bigtree/ — WGA “big tree” helpers (notebook + merge script).
    • scripts/wga/reprise/ — repeat evaluation utilities (.py).

Supporting GitHub Repositories

Modified ATLAS to reduce memory leaks and support resume functionality

See Kakapo Repo (will be moved to GA when final)