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
Interpretable prediction of antimicrobial-resistance phenotypes from bacterial genomes using determinants, background and population structure.
Open BAMPSPANOPTICON
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 repositoriesRecently updated
Current public repositories.
This section is refreshed automatically from public GitHub repositories; private project repositories are never included.
PhyloCloud
Public analysis, software or training repository.
Open repositorySourceRunnerML
SourceRunnerML is an advanced machine learning pipeline for microbial source attribution using (cg)MLST data.
Open repositoryCcoli-ST10042-global
Public analysis, software or training repository.
Open repositoryLINwalker
Public analysis, software or training repository.
Open repositoryDebrecen-workshop-2026
Material for Hu_RIZON project workshop in Debrecen, 2026
Open repositoryMOMENTO-MethyLome
MEMENTO integrates methylation calls, genome sequence, methyltransferase repertoires, phase-variable loci and isolate metadata to identify methylotypes and their genomic and ecological determinants.
Open repositoryProtocols 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 filesAnalytical checkpoints
Questions we revisit across projects.
Reusable analysis is not only about software. These recurring checkpoints help connect quality control, population structure and uncertainty to the biological question being asked.
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.