SourceRunnerML
cgMLST-based Campylobacter source attribution with model comparison, grouped validation, bootstrap uncertainty and post-processing.
Open SourceRunnerMLResources
Open methods, code and practical project material.
Software
Open tools developed for bacterial population genomics.
BAMPS-ML
Interpretable prediction of antimicrobial-resistance phenotypes from bacterial genomes using determinants, background and population structure.
Open BAMPS-MLPANOPTICON
Population-aware exploration of pangenome structure, accessory variation, ecological signal and gene-family sharing.
Open PANOPTICONLINwalker
Hierarchical analysis of LIN-code population structure, reservoir diversity, MLST concordance and interspecies introgression.
Open LINwalkerICassigner
Conservative assignment of Acinetobacter baumannii international clones using core-genome phylogenies and retained uncertainty.
Open ICassignerPascoe Lab on GitHub
Browse current software, analysis repositories, training material and the version-controlled lab website.
View all repositoriesProtocols and platforms
Methods, project resources and shared infrastructure.
GETcampy laboratory procedures
Culture, identification, DNA extraction and harmonised laboratory workflows.
Open protocols.ioGETcampy sequencing procedures
Short- and long-read sequencing workflows and associated quality control.
Open protocols.ioPopulation annotation and PubMLST
Stable lineage nomenclature and linked typing resources for genomic surveillance.
Visit PubMLSTCampylobacter Control Campaign GitHub
Project websites, meeting resources and developing analysis workflows.
Open organisationCampylobacter Control Campaign
Science, protocols, consortium, governance, training and communication pages.
Visit CCCPascoe Lab logo
Download the bacterium mark and horizontal lock-up for presentations, posters and profile images.
Open logo filesLab guides
Convert practical knowledge into maintainable pages.
Rather than burying instructions inside a general “lab guides” page, future additions should be short, versioned guides with an owner, last-updated date, prerequisites and links to the underlying protocol or repository.
Genome assembly and QC
Input requirements, contamination checks, assembly metrics and reproducible reporting.
Pangenome and core alignment
Choosing thresholds, diagnosing failed clusters and preparing phylogenetic input.
Population structure and trees
Recombination-aware analysis, lineage annotation and figure-ready metadata.
AMR interpretation
Separating determinant detection, phenotype association and population-genomic evidence.
Source attribution
Training design, grouped validation, class imbalance, contextual data and uncertainty.
Principles
What makes a useful open resource?
Versioned
Changes are visible and older analyses remain reproducible.
Portable
Dependencies and compute requirements are explicit.
Interpretable
The biological purpose and assumptions are documented.
Owned
A named project or person is responsible for maintenance.