Wisent genome assembly

Set of scripts to run the analyses presented in Bortoluzzi et al. (2024), including:

1. Genome assembly of the wisent;
2. Repetitive sequence analysis (RepeatModeler + RepeatMasker);
3. Phylogenetic tree construction;
4. Synteny;
5. Alignment of short-read DNA samples;
6. Genome-wide heterozygosity and ROH;
7. Pangenome analysis.

The repository contains also scripts to run analyses that were not included in the final manuscript (e.g., treemix, admixture, MSMC, PCA, relatedness).

Requirements

python v3.8.16; R v4.0.2

Citation

Please cite the article below when using the pipeline/scripts in your research:

Chiara Bortoluzzi, Xena Marie Mapel, Stefan Neuenschwander, Fredi Janett, Hubert Pausch, Alexander S. Leonard. Wisent genome assembly uncovers extended runs of homozygosity and a large deletion that inactivates the thyroid hormone responsive gene. Communications Biology (2024). https://doi.org/10.1038/s42003-024-07295-y