seqafrica/zambia-course

Links and materials for the SeqAfrica Zambia training # Zambia Training 2-5 June 2025 Repository to hold notes, files and links for the Zambia training Home: ## Programme * Zambia training agenda ## Day 1 Slides * Day 1 Slides * Bioinformatics Basics Links * Blog explaining ONT sequencing * Nice animation of ONT sequencing * Illumina Sequencing by Synthesis video Exercise links * Mystery species (did we really find Asgard archaea?) * Bacterial Species identification ## Day 2 Slides * Day 2 Slides * Illumina Reads QC * FastQC Puzzles Links * MinKNOW Report (Land Rover Sequencing) * Nanoplot repository and Nanoplot Online (sequencing summary only) * QUAST site and WebQuast (currently down) Exercise links * (Optional: for command-line experimenters) Installing WSL (and EPI2ME) on Windows * Perform FastQC on MiSeq reads * ONT QC - Analysis of NanoPlot reports * Reads and assembly QC - MultiQC reports ## Day 3 Slides * Day 3 Slides * BAP Slides and BAP repository * Bioinformatics Recap Links * hAMRonization and hAMRonization_workflow Exercise links * AMR detection and typing with online tools * Build your own anything-finder ## Day 4 Slides * Day 4 Slides * Phylogeny Slides * Simulated Exercise Instructions and metadata template Links * Enterobase and documentation and the paper * On-line Grapetree and off-line installation instructions, installation on Windows * Some demo datasets are linked from here Phylogenetics Tutorials * SSI GenEpi practical * BEAST basics * Timetree tutorials * IQ-TREE Simulated Exercise * Data will be distributed on USB stick; discussion of results is here