This code are analyses that accompanies the Zampirolo et al. It consists of bash and R scripts reporting raw data processing, phylogenetic analyses and data visualization for metaDMG in R.
| File | Content |
|---|---|
| Holi.sh | Holi pipeline for quality check and mapping reads |
| Consensus_sequences.sh | Read extraction and mapping sequences for Bos and Ovis reads |
| pathPhynder | pahPhynder commands to infer SNPs based trees |
| Sourcetracker2 | Sourcetracker2 python script |
| MetaDMG_Rscript.R | Script for visualising metaDMG output |
| Supplementary_Figures.R | Script used for producing Supplementary Figures |
| Sourcetracker2_plot | Sourcetracker2 python script for producing proportion plots |