This repository originally contained code to run analyses and generate figures for the:
Pneumococcal Genome Library cgMLST Typing Scheme Manuscript
S. aureus cgMLST Typing Scheme Manuscript
M. catarrhalis cgMLST Typing Scheme Manuscript
Note
To generate the:
- MST cluster analysis, please refer to: Analysis --> Profile clustering section
- Pairwise Allelic Mismatches plot, please refer to: Figures --> Figure 2a and 2b
- Rand Index plot, please refer to: Figures --> Figure 4e
This repository contains two main folders: Analysis and Figures.
View folder contents
- Analysis - contains the code used to generate:
- the distance matrix
- the phylogenetic tree
- GPSC and Mandrake clustering
- Figures - contains the R code used to generate main and supplementary figures
| Publication | DOI |
|---|---|
| MGen 2024 |  |
| bioRxiv 2025 |  |
| bioRxiv 2025 |  |
Tip
Useful Links for LINcodes
Below are helpful resources to learn more about LINcodes (Life Identification Numbers):
https://pubmed.ncbi.nlm.nih.gov/35700230/
https://www.biorxiv.org/content/10.1101/2024.03.11.584534v1.full
Additional information about how PubMLST deals with LINcodes can be found here BIGSdb documentation chapter 5.24.
If you have any queries, suggestions or concerns, please contact Angela Brueggemann.
Distributed under the GNU General Public License v3.0. Please see LICENSE for more information.
Repository PUBLIC status since: 30/05/2024 |
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