Lab guides and protocols
Bioinformatics pipelines
Bioinformatics pipelines
Bioinformatics pipelines
Explore my work on GitHub, including my flagship repository:
- SourceRunnerML
A robust machine learning pipeline for microbial source attribution using (cg)MLST data.
You can explore more of my projects and contributions directly on GitHub.
GETCampy protocols
Bioinformatics pipelines
Bioinformatics pipelines
Our GETCampy program builds on a decade of collaboration to map the epidemiology, genomics, and transmission of pathogens such as Campylobacter. By sharing protocols and resources, we aim to generate knowledge that directly benefits the children most at risk.
- Laboratory protocols
- Sequencing protocols
- Protocols manuscript TBC
GHRU
Bioinformatics pipelines
GHRU
The NIHR Global Health Research Unit (GHRU) on Genomic Surveillance of Antimicrobial Resistance empowers laboratories across LMICs with scalable, standardized genomic workflows—spanning wet‑lab through bioinformatics—to support actionable AMR surveillance. The protocols include:
- Wet-lab SOPs: From genomic DNA extraction (e.g. with Nexttec
The NIHR Global Health Research Unit (GHRU) on Genomic Surveillance of Antimicrobial Resistance empowers laboratories across LMICs with scalable, standardized genomic workflows—spanning wet‑lab through bioinformatics—to support actionable AMR surveillance. The protocols include:
- Wet-lab SOPs: From genomic DNA extraction (e.g. with Nexttec single-step kits), quantification (Qubit), purity checks (NanoDrop), library prep (NEBNext Ultra II FS), through to sequencing setup and sample transport.
- Bioinformatics pipelines: Open‑access workflows using Nextflow and Docker for assembly, SNP‑phylogeny, MLST, and AMR gene detection (e.g., via ARIBA).