GETcampy laboratory procedures
Culture, identification, DNA extraction and harmonised laboratory workflows.
Open protocols.ioResources
Open methods, code and practical project material.
A route to protocols, workflows, data resources, training material and project websites.
GETcampy sequencing procedures
Short- and long-read sequencing workflows and associated quality control.
Open protocols.ioCampylobacter Control Campaign GitHub
Project websites, analysis pipelines and reusable genomic resources.
Open GitHubCCC member and public resources
Science, protocols, consortium, governance, training and communication pages.
Visit CCCPopulation annotation and pubMLST
Stable lineage nomenclature and linked typing resources for genomic surveillance.
Visit pubMLSTInteractive genomic epidemiology
Project-specific Microreact, phylogeny and data-exploration links can be curated here.
Visit MicroreactLab 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.