rki-mf1/2026-Workshop-HSPA-Tunisia

# 2026-Workshop-HSPA-Tunisia --- Go to Tutorials. --- # Short-Read Analysis of Bacterial Pathogens ## Overview As part of the Work Area **“Genomic Surveillance”** within the **Health Security Partnership in Africa (HSPA)** project, the Robert Koch Institute is organizing a bioinformatics workshop in **Tunis, Tunisia**. The intensive workshop will take place from **18 to 22 May 2026** at the **Hôpital Charles Nicolle (HCN)** in Tunis. The workshop aims to further strengthen biosecurity and integrated disease surveillance capacities, with a particular focus on the bioinformatic analysis of **short-read sequencing data for bacterial pathogens**. Participants will receive hands-on training in essential bioinformatics approaches, ranging from introductory Linux skills and data management to genome assembly, sequence typing, cgMLST, phylogenetic analysis, and antimicrobial resistance prediction. The final day will be dedicated to the analysis and discussion of participants’ own data. ## Workshop content The workshop will cover key components of a typical bioinformatics workflow for the analysis of raw short-read sequencing data from bacterial pathogens. The training will focus on practical, hands-on experience using Linux-based command-line tools and commonly used bioinformatics software environments. Main topics include: - Linux basics - data and software management - Conda environments and containers - read quality control - genome assembly - assembly quality control - MLST and cgMLST - Minimum Spanning Trees - antimicrobial resistance prediction - analysis of participants’ own data --- ## Learning objectives Upon completion of the workshop, participants will be able to: - use fundamental Linux command-line operations to navigate the file system and run bioinformatics tools - apply good practices for data organization and software management in bioinformatics workflows - perform read quality control and interpret QC results - assemble bacterial genome …