/WisentGenomeAssembly

Scripts and pipelines used in the preprint Bortoluzzi et al. (2024)

Primary LanguagePython

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