Reproducibility deposit (code, data, and figure scripts) for: "Resistance travels, virulence stays: the mobile genetic elements of multi-host Streptococcus agalactiae decouple horizontal resistance from vertical virulence"

This deposit contains the analysis code, input data tables, and figure-generation scripts accompanying the manuscript "Resistance travels, virulence stays: the mobile genetic elements of multi-host Streptococcus agalactiae decouple horizontal resistance from vertical virulence". The study reconstructs the mobilome of five complete, closed Oxford Nanopore genomes of Streptococcus agalactiae spanning fish (ST283, ST7), bovine (ST103), and human (ST24, ST12) hosts, and maps the virulence and resistance cargo onto each mobile element at nucleotide resolution. It finds that resistance and virulence are decoupled: all twelve acquired resistance determinants sit on Tn916/Tn5253-family integrative and conjugative elements, one shared intact between a fish and a bovine genome at 99.8% identity, while the virulence repertoire, the pilus vaccine antigens included, is chromosomal (175 of 176 determinants), and no single element carries both. Contents- code/01_prophages.ipynb, code/02_ICE_IS_integron_islands.ipynb, code/03_defence_and_carriage.ipynb: notebooks reproducing the prophage, integrative-element/insertion-sequence/integron/island, and anti-phage-defence/carriage-matrix analyses.- code/figures/make_figures.py: a self-contained Python (Matplotlib) script that regenerates every manuscript figure (Figures 1 to 6, Supplementary Figures S1 and S2, and both graphical abstracts) deterministically from the deposited data tables. No AI and no network access are involved.- data/: element inventories, resistome coordinates, prophage catalogue, insertion-sequence family matrix, defence census, carriage summary, per-element gene tables, and windowed GC and GC-skew tracks.- CITATION.cff, MANIFEST.sha256 (SHA-256 checksum for every file), and LICENSE files. Reproduce the figures: pip install matplotlib numpy, then python code/figures/make_figures.py. The notebooks document the full upstream bioinformatics pipeline; the five complete genome assemblies and raw Oxford Nanopore reads are deposited separately under NCBI BioProject. Licensing: the data and documentation are released under the Creative Commons Attribution 4.0 International licence (CC BY 4.0); the code is additionally released under the MIT License. See LICENSE-data.txt and LICENSE-code.txt.