Scripts to analyse within-host evolution during S. aureus colonisation and infection.
The analysis was published in eLife:
Giulieri SG, Guérillot R, Duchene S, Hachani A, Daniel D, Seemann T, Davis JS, Tong SYC, Young B, Wilson DJ, Stinear TP, Howden BP. Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections. eLife. 2022 Jun 14;11:e77195. DOI:10.7554/eLife.77195.
Note that the shell scripts should be run in one of the following conda environments:
conda snippy (conda install snippy, conda install prokka)
conda R (conda install R)
conda base (conda install cd-hit, conda install seqkit, conda install csvtk)