Module 1: Introduction to basic Unix commands

This module introduces essential Unix shell commands and concepts required for working in computational environments. You will learn how to navigate file systems, manipulate files, and execute basic commands commonly used in bioinformatics workflows.

Tutorial	Slides	Description	Learning Objectives	Estimated Time
Introduction to basic Unix commands		This is the introduction to the basic shell commands.	Describe key reasons for learning shell. Navigate your file system using the command line. Access and read help files for `bash` programs and use help files to identify useful command options. Demonstrate the use of tab completion, and explain its advantages.	2H

Module 2: Basecalling ONT data

This module introduces the preprocessing workflow for Oxford Nanopore Technologies (ONT) sequencing data, starting from raw signal files. You will learn how to perform basecalling, assess read quality, and prepare high-quality sequencing reads for downstream genome analysis.

Tutorial	Slides	Description	Learning Objectives	Estimated Time
Basecalling and QC of ONT data		This tutorial introduces the preprocessing workflow for Oxford Nanopore Technologies (ONT) sequencing data, from raw signal files to quality-controlled reads for downstream analysis.	Understand the physical and electrical principles of Nanopore sequencing and signal recording. Explain the transition from early HMM-based basecallers to modern Transformer-based models like Dorado. Differentiate between Fast, HAC, and SUP basecalling models and interpret Phred quality scores. Compare the data architecture of HDF5-based FAST5 and Apache Arrow-based POD5. Inspect raw metadata and convert legacy FAST5 datasets into the production-standard POD5 format. Apply fastplong to trim adapters and filter long reads by length and quality. Align long and short reads to a reference genome using minimap2 and BWA, and process files via samtools for IGV visualization.	2H

Module 3: Metagenomics assembly

This module introduces genome assembly approaches for long-read and short-read sequencing data. You will learn how to assemble prokaryotic genomes from ONT and Illumina reads, evaluate assembly quality, improve assemblies through polishing and hybrid assembly strategies, and assess the final assembly results. The module also provides an introduction to metagenome assembly workflows using dedicated bioinformatics tools.

Tutorial	Slides	Description	Learning Objectives	Estimated Time
Metagenome Assembly: concepts and hands-on comparison of assemblers		This tutorial introduces the principles and challenges of metagenome assembly, including de Bruijn graph-based approaches, k-mer selection, and metagenome-specific assembly strategies. You will apply several assemblers, including Velvet, MEGAHIT, metaSPAdes, IDBA-UD, and Ray, and compare their assembly performance.	Recognize common sources of assembly ambiguity, such as repeats, sequencing errors, and uneven species abundance. Run multiple metagenome assemblers on sequencing reads and generate assembly statistics.	6H
Assembly and assembly evaluation (hands-on)		This tutorial demonstrates how to assemble a prokaryotic genome using Oxford Nanopore and Illumina sequencing data, evaluate assembly quality, improve assemblies through polishing and hybrid assembly approaches, and assess the final results.	Reconstruct a bacterial genome using Flye and SPAdes, and visually evaluate assembly graph topologies in Bandage. Execute the multi-step Polypolish workflow (all-mapping, filtering by insert size, and polishing) to correct homopolymer indels.	2H

Module 4: Genome annotation

This module covers the functional annotation of bacterial genomes. You will learn how to identify genomic features, predict genes, assign functional information, and interpret genome annotations using commonly used annotation tools.

Tutorial	Slides	Description	Learning Objectives	Estimated Time
Prokaryotic Genome Annotation (hands-on)		Learn the steps of prokaryotic genome annotation by generating and comparing annotations with Prokka and Bakta. The tutorial also introduces EDGAR for comparative genome analysis, including core-genome, pan-genome and ortholog identification.	Generate comprehensive genome annotations with Prokka and Bakta, and interpret differences in functional naming and hypothetical protein rates. Explain how comparative genomics frameworks like EDGAR identify core genomes, pan-genomes, and unique singleton genes.	2H

Module 5: Long-Read Metagenomics using the Metagenomics-Toolkit

This module introduces long-read metagenomics analysis using the Metagenomics-Toolkit. You will learn how to prepare ONT sequencing data, run the initial analysis workflow, and explore the first steps of metagenomic data processing and interpretation.

Tutorial	Slides	Description	Learning Objectives	Estimated Time
Introduction to Long-Read Metagenomics using the Metagenomics-Toolkit		This tutorial will guide you through the first steps to run the Metagenomics-Toolkit on ONT data	Understand the execution syntax and command-line parameters of Nextflow-based workflows. Configure a YAML parameter file for long-read metagenomic quality control and assembly steps. Navigate the hierarchical per-sample and aggregation output structures of the Metagenomics-Toolkit.	1H