Reproducibility deposit: Quantitative microbial risk assessment of foodborne invasive Streptococcus agalactiae from raw freshwater fish, informed by genomic source attribution

Abstract

Code, parameters, and derived data to reproduce the quantitative results and figures of the associated manuscript. The quantitative microbial risk assessment (forward, sensitivity, value-of-information, control-target, and outbreak inverse models) regenerates from documented parameters by code/qmra_model.py, which self-checks every statistic against the reported values. The genomic source attribution is reproduced by code/attribution_pipeline.ipynb, a self-contained seeded notebook that downloads the 1,742 public assemblies from NCBI by accession, builds wgMLST and alignment-free k-mer features, and runs the random-forest classifier under lineage, coarse-cluster, completeness, and BioProject blocking. Derived intermediates, the full 1,742-accession genome-panel table, a data dictionary, and the figure engine are included so all figures regenerate at 600 dpi. Software is released under MIT; the derived data files under CC-BY-4.0. The underlying genome assemblies are public; only accessions are distributed.