/Citrobacter

A repository containing analysis and associated scripts for a manuscript on a collection of Citrobacter

Primary LanguageR

Environmental Citrobacter

This GitHub page accompanies a manuscript currently under review.

There are additional scripts available that detail other analyses performed that didn't make it into the final analyses, however the most relevant scripts to look at (as it pertains to the manuscript) are:

  1. Markdown/Figure_1_internal_tree_w_refseq_refs.Rmd
  2. Markdown/Figures_2_4_5_internal_only.Rmd
  3. Markdown/SKA_analysis_100_SNPs.Rmd
  4. Markdown/QC_workflow.Rmd

Genomic data is in results, metadata and other info is in delims, QC data is in QC_summaries and bacsort contains files used in the running of BacSort for phylogenetic assignment