SG17-135

This is a repository containing scripts for the generation of figures within a publication on an XDR strain of Salmonella sourced from an Australian Gull.

DOI: 10.1128/mSphere.00743-20

Directory	Contents
analysis	Output of bioinformatic analysis tools
assemblies	Genome assemblies from Enterobase
fasta_dbs	Nucleotide databases uses in abricate
figures	Final figures of manuscript
flags	Flag images used in generation of figures
logs	Logs generated during bioinformatic analyses
metadata	Metadata on samples under analysis
scripts	Scripts used for post processing of data and data visualisation
supplemental_material	Supplementary material for the manuscripts

analysis

abricate

Contains abricate output, concatenated from each resulting output file:

abricate.txt - Contains abricate data on plasmid, virulence and AMR gene carriage
abricate_PAIs.txt - Contains abricate data on Salmonella Pathogenicity island (SPI) and pathogenicity associated island (PAI) carriage

snp_outputs

Contains output of snplord pipeline

Agona195 - Contains snp matrix and phylogenetic tree for large subset of Agona genomes (n=195)
Agona80 - Contains snp matrix and phylogenetic tree for small subset of Agona genomes closely related to SG17-135 (HC5:4181 strains) (n=80)

pointfinder

Contains output of pointfinder analysis

pointfinder_results.txt - lists AMR associated SNPs associated with particular genomes from the Agona195 subset

scripts

Figure 1.R

This script is used to generate Figure 1, as well as Supplementary Table 1 which combines Metadata and Genotypic data of samples

Figure_2.R

This script is used to generate Figure 2, as well as Supplementary Table 4 which combines lists the co-association of AMR genes and IncX scaffolds

Random_subset_IncX.R

This script is used to (pseudo)randomly select 10 IncX-positive strains from the Agona80 subset for analysis using BRIG

SPI-analysis.R

This script is used to classify strains as SPI/PAI positive or negative based on >=60% (discontiguous) coverage and >=95% nucleotide identity for a given genetic element

Majestic Seagull

R Session info

R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 
 
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] reshape2_1.4.3  readr_1.3.1     dplyr_0.8.3     magrittr_1.5    pheatmap_1.0.12 ggtree_1.16.6  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2         pillar_1.4.2       compiler_3.6.0     RColorBrewer_1.1-2 plyr_1.8.4         tools_3.6.0        zeallot_0.1.0      jsonlite_1.6      
 [9] tidytree_0.2.6     tibble_2.1.3       gtable_0.3.0       nlme_3.1-141       lattice_0.20-38    pkgconfig_2.0.2    rlang_0.4.0        rstudioapi_0.10   
[17] rvcheck_0.1.3      yaml_2.2.0         parallel_3.6.0     treeio_1.8.2       stringr_1.4.0      vctrs_0.2.0        hms_0.5.1          grid_3.6.0        
[25] tidyselect_0.2.5   glue_1.3.1         R6_2.4.0           tidyr_0.8.3        ggplot2_3.2.1      purrr_0.3.2        scales_1.0.0       backports_1.1.4   
[33] assertthat_0.2.1   ape_5.3            colorspace_1.4-1   labeling_0.3       stringi_1.4.3      lazyeval_0.2.2     munsell_0.5.0      crayon_1.3.4

maxlcummins / SG17-135