cgMLST-comparison

Comparing distances for cgMLST

Methods

1. Survey different cgMLST methods
2. Have an existential crisis that each cgMLST method has a slightly different database that I cannot account for
3. Receive validation datasets from PulseNet (not publicly available)
4. Run cgMLST using each method
5. Create pairwise distances using distance.* methods in the lskScripts repo
6. Record
   • number of alleles in common
   • number of loci compared
   • identity = alleles / loci

Results

1. Found suitable callers
   • EToKi
   • ChewBBACA
   • ColorID
2. Created scatter plots with goodness of fit

dataset	link
S. enterica	notebook
L. monocytogenes	notebook
C. jejuni	notebook
E. coli	notebook