Presented here are the scripts used for data analyses in each data chapter of my thesis. Within each directory is a brief overview of chapter contents and details about each of the tools used. In recognition of Indigenous Data sovereignty of data related to culturally significant species, any sample IDs have been redacted from these scripts.

For a brief outline of chapter contents:

A nearly complete short-read resequence data set and high quality reference genome were used to investigate structual variantion (SVs) in the critically endangered kākāpō (Strigops habroptilus). Structural variants were called using the Delly, Manta and SMOOVE pipelines.

Whole-genome short-read resequence data were aligned to the chromosomally assembled reference genome for the common tern (Sterna hirundo) to explore relative levels of population diversity and differentiation for two fairy tern taxa.

Long-read Oxford Nanopore sequence data was used for de novo genome assembly. Genomes were assembled using FLYE v2.8.3. Graphs were constructed using pggb v0.2.0, and odgi v0.6.3.

Publications associated with this thesis include: Published Perspective in the Molecular Ecology Special Isl: Whole-genome sequencing in molecular ecology 2021.