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.
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 |
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
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)
Contains output of pointfinder analysis
- pointfinder_results.txt - lists AMR associated SNPs associated with particular genomes from the Agona195 subset
This script is used to generate Figure 1, as well as Supplementary Table 1 which combines Metadata and Genotypic data of samples
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
This script is used to (pseudo)randomly select 10 IncX-positive strains from the Agona80 subset for analysis using BRIG
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
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