Repo for code associated with pT181 project (Phillips et al. 2025, bioRxiv) - https://www.biorxiv.org/content/10.1101/2025.09.14.675889v1 "Transition of Staphylococcus aureus tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years"
All genomes used in this study are publicly available
finding pT181
- blast.1.sh - find pT181 in genomes
- getcol.1.sh - get samples clearing 4400bp threshold, start position
PCN
- blast.2.sh - find known chromosomal genes & tetK in genomes
- bwa.sh - fastq to sam
- samtools-view-sort-depth.sh - read depth at all sites
- depth+conlen.sh - script for avg depth calculations & contig length only (post-samtools)
- glmm.pcn.reduced.Rmd - Rmd for GLMM for copy number; copy number x strain * bioproject
phitest
- ska.7988.sh - make skf file and alignment of all pT181 contigs (n = 7988)
- phitest.sh - perform phi test for recombination
rotation (of the plasmid)
- samtools.sh - start all plasmids at same spot relative to blast hit
- prelin.sh - remove extra header; prep for picard
- picard.sh - normalize pt181 contigs
trees
- iqtree.sh - commands for building trees
- cds.partitions - regions of seq to be partitioned for CDS tree
- *.contree & *.treefile - trees, newick format
clinker
- gettingthecontigs.sh - pull out SRA contigs to be used for clinker figure
- bakta.sh - annotate contigs
- genes.red.csv - geneIDs for figure
- clinker.sh - run clinker
snippy
- snippyloop.sh - run snippy for pt181 contigs
filesforR
- pT181-reunifyG.Rmd - Rmd for PCN calculations, figuremaking, stats
- allthebacteria-sccmec.tsv - output from sccmec tool run on AtB
- pubmet-* - metadata for SRA runs
- 14.description.ncbi.txt - description for 14 pT181+ complete genomes
- staphopia_v2_all_report.txt in Zenodo for Raghuram et al. 2024 msystems (https://zenodo.org/records/10471309)
- isolate_substrain_strain_freq_st_CC.tsv same as above
- dnaA_start_coords.gfs from https://github.com/VishnuRaghuram94/SCAPE/blob/main/timsfigsData.zip