Skills
Technical toolbox.
A working summary of the methods, tools, and languages I use day to day.
Bioinformatics
- Command-line scripting (Linux/Bash)
- Bacterial genomics: QC, assembly, annotation
- AMR gene detection: Abricate, CARD, ResFinder
- Comparative genomics & pangenome analysis (Roary)
- Genomic surveillance: Pathogenwatch, Kleborate
- 16S microbiome and metagenomics
- RNA-Seq and single-cell transcriptomics
Data Science
- R, Python, MATLAB
- Statistical analysis (SPSS, GraphPad Prism)
- Geospatial data analysis and mapping
- Machine learning workflows in R/Python
- Data visualisation (ggplot2, matplotlib, seaborn)
- Reproducible reporting (R Markdown, Quarto)
Wet lab
- Bacterial culture and identification
- DNA extraction and quantification
- Whole-genome sequencing on Oxford Nanopore MinION
- Phenotypic AMR testing