Collection of Tutorials

Explore our curated collection of training materials covering a wide range of topics in cloud computing, bioinformatics, and data science. These tutorials are designed for hands-on learning and support both beginners and advanced users.

For some tutorials, multiple versions are available, allowing you to access different iterations of the same lesson. By default, select the "main" version to access the most up-to-date materials. Other versions may be useful for following older course editions or reproducing previous training sessions.

Lesson materials are all available online under a CC BY 4.0 license, for self-directed study or for adaptation and re-use in your own training sessions.

Unix

Tutorials focused on basic Unix / Linux commands and shell usage.

Tutorial Versions Slides Description Contributors Estimated Time
Introduction to basic Unix commands main
spring-school-2024 		spring-school-2024 (PDF) This is the introduction to the basic shell commands. 2H

Cloud computing

Tutorials focused on using the de.NBI Cloud infrastructure and project types.

Tutorial Versions Slides Description Contributors Estimated Time
SimpleVM Workshop main Tutorial shows how to identify pathogenic bacteria within publicly available metagenomic datasets and scale up a bioinformatics workflow using SimpleVM. 2H
BiBiGrid Hands-on main Tutorial shows how to provision and operate a small HPC cluster on OpenStack using BiBiGrid 2H

Cloud application deployment

Tutorials in this group offer hands-on experience in building, containerizing, and deploying applications from local development environments to the cloud.

Tutorial Versions Slides Description Contributors Estimated Time
Build a Simple Dataset Web App on EMBL Cloud Infrastructure main Learn to create and deploy a web application using Python, Streamlit, Docker/Podman, and Kubernetes on EMBL cloud computing infrastructure 2H

Machine Learning on Cloud infrastructure

Tutorials focused on setting up machine learning toolkits and applications on cloud infrastructure.

Tutorial Versions Slides Description Contributors Estimated Time

PATCH Tutorials

Tutorials in this group contain learning material about the tools contained inside the pangenomics toolbox PATCH

Tutorial Versions Slides Description Contributors Estimated Time

Genomics and Metagenomics

Tutorials focused on handling of genomics and metagenomics sequencing data

Tutorial Versions Slides Description Contributors Estimated Time
Metagenomic Quality Control & Preprocessing main This tutorial introduces the workflow for assessing sequencing quality with FastQC, trimming adapters, and removing low-quality bases using fastp and Cutadapt. 1H
Metagenome Assembly: concepts and hands-on comparison of assemblers main
main 		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. 1H
Assembly Evaluation main This tutorial introduces the workflow for evaluating metagenomic assemblies by mapping reads back to contigs and computing assembly metrics using MetaQUAST. 1H
Metagenomic Binning and Classification main This tutorial introduces the workflow for clustering assembled metagenomic contigs into genomes (binning), evaluating their quality, and assigning taxonomic labels using modern bioinformatics tools. 1H
Introduction to the Metagenomics-Toolkit main This tutorial will guide you through the first steps to run the Metagenomics-Toolkit on paired-end metagenomic sequencing data. It covers pipeline configuration, execution, result inspection, and interactive analysis with Jupyter notebooks. 1H
Basics of Amplicon Quality Processing main Basic steps to do manually quality processing of 16S data step by step with individual tools instead of using integrated solutions like qiime2 / dada2 / deblur. 2H
Basecalling and QC of ONT data main This tutorial introduces the preprocessing workflow for Oxford Nanopore Technologies (ONT) sequencing data, from raw signal files to quality-controlled reads for downstream analysis. 2H
Introduction to Long-Read Metagenomics using the Metagenomics-Toolkit main This tutorial will guide you through the first steps to run the Metagenomics-Toolkit on ONT data 1H
Prokaryotic Genome Annotation (hands-on) main 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. 2H
Assembly and assembly evaluation (hands-on) main 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. 2H

Data Management on the Cloud

Tutorials focused on data management best practices, solutions on the Cloud, including how to adapt a solution to the cloud (Kubernetes and S3 storage)

Tutorial Versions Slides Description Contributors Estimated Time
Basic Data Management in the de.NBI Cloud main Basic Data Management in the de.NBI Cloud. Intended for a cloud-naive audience. 8H
Using the cross-domain Data-Management Platform repository main A step-by-step overview of how to use the repository. 40M

Incubator

Tutorials in this group are under review.

Tutorial Versions Slides Description Contributors Estimated Time
RDM Microbial Training Course main
Ansible main
Deploying Machine Learning workflow using FastAPI main 3H
Setting up ML project in the cloud infrastructure main Transform a trained model into an online service with a UI using Streamlit. 5H
PanBench main Introduction to using the web interface of panbench.eu 10M