Reproducibility deposit for the complete genomes of fish-, human- and buffalo-associated Streptococcus agalactiae: analysis code, reference-context genome list and derived outputs

Reproducibility deposit accompanying the manuscript "Complete genomes of fish-, human- and buffalo-associated Streptococcus agalactiae uncouple host of isolation from lineage and resolve chromosomal architecture missed by short-read assembly." The archive lets a reviewer or reader reproduce every derived result and figure from the deposited inputs. It contains the analysis notebooks (read QC and assembly, read-mapping coverage validation, CheckM2 completeness and the Gubbins recombination screen, inversion-breakpoint read depth, and a notebook that regenerates every figure under one colour-blind-safe palette and runs the long-branch model-sensitivity and AU/SH topology test and the MOB-suite plasmid screen), the shared figure-style module, the list of the 100 public reference-context genomes with their accessions, and the MOB-suite result for the five genomes. Software versions and key parameters are recorded in ENVIRONMENT.md (IQ-TREE 3.1.2, ModelFinder -m MFP, GTR+F+I+R6, seed 973811). The five complete genome assemblies and their raw Oxford Nanopore reads are archived at NCBI under BioProject PRJNA_XXXXXX (per-genome and SRA run accessions in Table 1 of the manuscript). Code is released under the MIT licence and data under CC-BY-4.0.