Pipelines and analysis codes for the following paper: Tan, H. Z., Scherer, P., Stuart, K. C., Bailey, S., Lee, K. D., Brekke, P., Ewen, J. G., Whibley, A., Santure, A. W. (2024). A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta). Heredity https://doi.org/10.1038/s41437-024-00711-3

Folder names correspond to the sections in 'Materials and methods'.

Linkage map results showing the map positions of each marker is in folder 'Results_hihi_linkage_map'.

Unless otherwise stated, codes were ran via Jupyter on New Zealand eScience Infrastructure (NeSI).