The course is organised into six weekly modules, delivered consecutively from October to December.

Week 1 — UNIX and the Command Line. An introduction to working on the Linux command line: navigating the filesystem, redirection and wildcards, variables and for-loops, and writing simple shell scripts. The week ends with an introduction to cloud computing on CLIMB, Conda/Mamba environments, and JupyterHub.

Week 2 — DNA Sequencing with NGS Covers the fundamentals of sequencing technologies, both long-read (Nanopore) and short-read (Illumina), the file formats used to store sequencing data (FASTQ, SAM/BAM), and how to perform basic quality control on a sequencing run.

Week 3 — From Sequence to Consequence Focuses on bacteriophage genomics, taking sequence data through to biological interpretation, following the Adriaenssens lab’s phage genomics material at a flexible, hands-on pace.

Week 4 — Comparative Genomics Introduces mapping and variant calling, pan-genome analysis and mobile genetic elements, genome comparison and structural variation, culminating in a session on outbreak investigation.

Week 5 — Metagenomics Covers microbiome genomics approaches (profiling versus de novo assembly), quality checks specific to metagenomic data, contig binning, strain tracking with k-mer sketches, and functional/metabolic pathway characterisation of microbial communities.

Week 6 — Functional Analysis Explores bacterial behaviour and image analysis, transcriptomics and RNA-seq, and transposon mutagenesis (TraDIS), concluding with a wrap-up of the whole course.

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