Pneumococcal Genome Library cgMLST Typing Scheme

Overview

This repository contains the code used to run analyses and generate figures for the following manuscript:

Microbial Genomics Manuscript

Warning

The manuscript is still under review, therefore the link goes to a blank page but this will be updated once the paper is published.

Note

This repository contains modified code from the original repository that accompanied the pre-print publication in bioRxiv. The original repository and code was authored by Duncan Berger. To view the original repository, please click on the following links:

Brueggemann Lab Repository (forked from Duncan Berger)	Duncan Berger's Repository

Codebook

This repository contains two main folders: Analysis and Figures.

graph TD;
repo[This Repository]
dist[Distance Matrix]
tree[Phylogenetic Tree]
clust[GPSC Clustering]
clust2[Mandrake Clustering]
repo-->Analysis;
Analysis-->dist;
Analysis-->tree;
Analysis-->clust;
Analysis-->clust2;
dist-->Manuscript;
tree-->Manuscript;
clust-->Manuscript;
clust2-->Manuscript;
repo-->Figures;
Figures-->Manuscript;
dist-->Figures;
tree-->Figures;
clust-->Figures;
clust2-->Figures;

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View folder contents

1. Analysis - contains the code used to generate:
1. the distance matrix
2. the phylogenetic tree
3. GPSC and Mandrake clustering
2. Figures - contains the R code in markdown format used to generate main and supplementary figures

License

Distributed under the GNU General Public License v3.0. Please see LICENSE for more information.

Publication History

Publication	DOI
bioRxiv 2023

Tip

Reference: Jansen van Rensburg MJ, Berger DJ, Fohrmann A, Bray JE, Jolley KA, Maiden MC, Brueggemann AB. Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure. bioRxiv. 2023:2023-12.

Important

Please click here to access more information about life identification number (LIN) codes. Additional information about how PubMLST deals with LINcodes can be found here - BIGSdb documentation chapter 5.24.

Quality control (QC) of genome sequence data is vital for robust analyses. Please see the pre-print publication in bioRxiv (and Supplementary Data Table 2 in particular) for details about the QC metrics derived from the analysis of the PGL genomes.

Contact

If you have any queries, suggestions or concerns, please contact Angela Brueggemann.

Repository PUBLIC status since: 30/05/2024