Includes all code necessary to reproduce the analysis of our 2018 comparative genomic analysis of Carbapenemase producing bacteria isolated in Basel. Folders include:
- assembly/ -- Includes all python scripts used to assembly all genomes on the SciCORE cluster, as well as run all error QC statistics as described in the manuscript
- plotting/ -- Includes all python scripts used to generate the figures of the paper.
- synteny/ -- Includes all python scripts used to perform the synteny analyses described in the paper.
- coreGenome/ -- Includes all python scripts used to perform the quantification of homologous recombination within the core genome.