seqafrica/malawi-course

Links and materials for the SeqAfrica Malawi training # Malawi Training 4-7 March 2025 Repository to hold notes, files and links for the Malawi training Home: ## Programme * Malawi training agenda ## Day 1 Slides * Day 1 Slides * Bioinformatics Basics * BAP Slides and BAP repository Links * Blog explaining ONT sequencing * Nice animation of ONT sequencing 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 * Illumina Sequencing by Synthesis video * Land Rover Sequencing Report Exercise links * (Optional: for command-line experimenters) Installing WSL and EPI2ME on Windows * FastQC analysis of MiSeq reads * Interpret QC analysis of Malawi data ## Day 3 Slides * Day 3 Slides * Bioinformatics Recap Links * hAMRonization and hAMRonization_workflow Exercise links * Build your own anything-finder * AMR detection with online tools ## Day 4 Slides * Day 4 Slides Links * Enterobase and documentation and the paper * On-line Grapetree and off-line installation instructions * Grapetree "Agona" demo data: cgMLST and metadata Phylogenetics Tutorials * SSI GenEpi practical * BEAST basics * Timetree tutorials * IQ-TREE Exercise * Data will be distributed on disk; discussion of results is here