quote-RCandy-quote: Gubbins recombination data

In ChrispinChaguza/RCandy: RCandy: an R package for rapid visualisation of homologous recombination events in bacterial genomes

Gubbins recombination data

Description

This dataset provides an example phylogenetic tree, strain metadata, reference genome and recombination events for 170 Streptococcus pneumoniae isolates collected globally belonging to the multilocus sequence typing (MLST) clone ST320.

Usage

data("RCandy")

Format

A list containing four data frames:

tree

phylo: Phylogenetic tree in ape's phylo format

metadata

data frame: Data frame containing metadata for the strains in the tree

gubbins.GFF

data frame: Data frame containing recombination events identified in each strain (GFF format)

refgenome.GFF

data frame: Data frame containing genomic features in the reference genome (GFF format)

A list containing pre-loaded phylogenetic tree, taxon metadata, Gubbins GFF file, and reference genome GFF file

Source

Gladstone RA, Lo SW et al. International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact. EBioMedicine. 2019 May;43:338-346. doi: 10.1016/j.ebiom.2019.04.021. Epub 2019 Apr 16. PMID: 31003929; PMCID: PMC6557916.

The Global Pneumococcal Sequencing (GPS) Consortium: https://www.pneumogen.net/gps/

The reference whole genome sequence was obtained from GenBank (accession number: NC_010380): https://www.ncbi.nlm.nih.gov/nuccore/NC_010380.1.

ChrispinChaguza/RCandy documentation built on June 23, 2022, 1:03 p.m.