Online Course - A Practical Introduction to NGS Data Analysis
Quality Control, Read Mapping, Visualization and DNA Variant Analysis

Advance your research. Understand NGS and analyze sequence data yourself.

In a nutshell

  • Learn the essential computing skills for NGS bioinformatics
  • Understand NGS technology, algorithms and data formats
  • Use bioinformatics tools for handling sequencing data
  • Perform first downstream analyses for studying genetic variation

February 28 - March 1, 2024
9 am - 5 pm (CET UTC+1)


52 votes

The purpose of this workshop is to get a deeper understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. The participants will be trained on understanding their own NGS data, finding potential problems/errors therein and finally perform their first downstream analysis (variant calling). In the course we will use a real-life NGS dataset from the current market leader illumina.

All workshop attendees will be enabled to perform important first tasks of NGS data analysis themselves. The course layout has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this fast evolving research topic.

The online course will make use of a web conferencing system. Hands-on NGS analysis will be performed in an interactive browser-based data analysis platform. Before the course, you will get a printed manuscript.

Get trained by experts

Our trainers have a proven record of academic and/or industrial experience in NGS data analysis. Because up-to-date expert knowledge is needed to answer your questions and know what is important in the field.

Open source NGS tools

We only use open source tools that are free to use. We try to showcase and compare different tools (e.g. NGS mappers), since not every software fits with every task/question.

Learn effectively with well-curated materials

For a optimal learning experience we carefully prepare our learning materials and example data.

This workshop has been adapted to the needs of beginners in the field of NGS bioinformatics and comprises this three course modules:

  1. NGS Technologies:
    Different methods of NGS will be explained and compared, together with the consequences for data analysis. The most important notations and an overview over various applications will be given.
  2. Practical Bioinformatics (with Linux):
    This module will introduce the essential tools and file formats required for NGS data analysis. It helps to overcome the first hurdles when entering this (for NGS analyses) unavoidable operating system.
  3. Introduction to NGS data analysis:
    Important first NGS analyses tasks will be explained and performed. This module covers essential knowledge for analysing data of different NGS applications.

Detailed Course Program

NGS Technologies

  • Introduction to sequencing technologies from a data analysts view
  • Common NGS data analysis issues
  • Applications of sequencing technologies
  • Notations and NGS Terminolgy

Practical Bioinformatics (with Linux)

  • Introduction to the command line and important commands
  • Combining commands by piping and redirection
  • Introduction to bioinformatics file formats (e.g. FASTA, BED) and databases (e.g. UCSC)
  • Usage of important bioinformatics toolkits (BEDtools)

Introduction to NGS data analysis

  • Raw sequence files (FASTQ format)
  • Preprocessing of raw reads: quality control (FastQC), adapter clipping, quality trimming
  • Introduction to read mapping (Alignment methods, Mapping heuristics)
  • Read mapping (BWA, BWA-MEM, Bowtie2, STAR, segemehl)
  • Mapping output (SAM/BAM format)
  • Usage of important NGS toolkits (samtools)
  • Mapping statistics
  • Visualization of mapped reads (UCSC)
  • DNA variant calling
  • Variant Call File Format (VCF)
  • Filtering DNA variants


Dr. David Langenberger (ecSeq Bioinformatics GmbH)
David started working with small non-coding RNAs in 2006. Since 2009 he uses NGS technologies to investigate these short regulatory RNAs as well as other targets. He has been part of several large NGS projects, for example the International Cancer Genome Consortium (ICGC). Publications

Dr. Adam Nunn (ecSeq Bioinformatics GmbH)
Adam is an expert bioinformatician skilled in developing data analysis pipelines. He specializes in whole genome DNA-Seq, de-novo genome assemblies, bulk RNA-Seq, and single-cell RNA-Seq. Publications

Dr. Mario Fasold (ecSeq Bioinformatics GmbH)
Mario works in the analysis of microarray data since 2007 and developed several bioinformatics tools such as the Bioconductor package AffyRNADegradation and the Larpack program package. Since 2011 he specialized in the field of NGS data analysis and helped analysing sequencing data of several large consortium projects.


The target audience is biologists or data analysts with no or little experience in analyzing NGS data. A fundamental understanding of molecular biology (DNA, RNA, gene expression, PCR, ...) is assumed.

Previous knowledge of Linux & Bioinformatics is not required. Yet these tutorials might be a helpful preparation.

A current desktop computer / laptop with an up-to-date browser (Firefox or Chrome) is required.

  •   Printed course materials
  •   High-performance cloud computer (accessed via browser)
  •   Downloadable Live-Linux system with pre-installed NGS tools for seamless continuation / repetition after the course
  •   Certificate

  •   Hands-on use of essential NGS tools to see where the stumbling blocks are
  •   Our assistants can help you and provide feedback you on the spot
  •   No previous installation of software necessary
  •   Continue practicing on your own using our Live-Linux system and the printed manuscript


Location: Online
Language: English
Available Seats: 25 (first-come, first-served)

Registration Fee: 879 EUR (excluding VAT)

Key dates

Opening Date of Registration: October 16, 2023
Closing Date of Registration: February 20, 2024
Workshop: February 28 - March 1, 2024 from 9 am to 5 pm (CET UTC+1)

Find out what time it is at your location: Time Difference

"The handout, as well as the setting (terminal login and zoom) was absolute in time and accurate. The frame of the workshop equips one with enough information to get started for the first NGS data set analysis. The four trainers were super friendly, open to help and most competent. The course is highly recommended." André Riedl, Bavarian Nordic, Germany

"I was blown away by the Course. I did some similar courses in the past and got little or nothing from them. This workshop gave me the ability to understand what is actually written in the command line, how to read it and the data and how to do the simple analysis myself. I am not terrified of the command line anymore. Actually, I can't get enough of it now. Also, I tried to reproduce the whole pipeline on my own data and actually got it all done using the knowledge and the resources from the workshop. All I need now is experince in reading the analysis :-D" Sanja Duvnjak, Croatian Veterinary Institute, Croatia

"The course is very well structured and focuses all the main topics on NGS data analyses, with the appropriate detail for beginners. The tutors are excellent and very friendly and mentioned a lot of details, which only experienced users know. I have learnt a lot! " Alexandra Rosa, University of Madeira, Portugal

When you register for this workshop you are agreeing with our Workshop Terms and Conditions. Please read them before you register.


What you need:

  • A computer with one of the following operation systems: Windows 7 or later (incl. Windows 10), Mac OS X 10.13 or later.
  • One of the following web browsers: Edge 42 and later, Chrome 65 or Later, Firefox 48 or Later.
  • A microphone and loudspeakers/headphones.

  The course cannot be run on phones, tablets and similar handheld devices.


We will start every morning at 9am sharp and work together until 5pm in the afternoon. There will be regular short breaks and a longer break at lunchtime.

As this is a live broadcast, you cannot pause the course and continue later. The individual exercises build on each other, so you should not leave in between.


No, you do not have to install any software to follow the course. You will get access to a high performance computer in the cloud, which you can easily log into using an in-browser console. All necessary programs are already installed on this computer. This way, we can start right away.


Of course we'll help you. If such a case should occur, we have assistants in the virtual room whom you can contact via chat. They can discuss your issue in a separate room/chat. They can also dial into your in-browser console and see exactly the same as what you see. This way they can help you directly and without much detour.

Note: The assistent can only see your in-browser terminal window but nothing else and also do not have any access to your computer.


A few days before the course we will send you the manuscript by mail. After the course, you will receive a download link for our Live-Linux system with pre-installed NGS tools. When you start this with a virtualization tool (such as the free VirtualBox), a live version of Linux will be running on your computer where you can repeat and/or practice all the tasks of the course.


We have tried to keep the differences between the online and the attendance courses as small as possible.

Before the event: If you like to travel and get to know new cities, you will miss that in an online course. But, with an online workshop, you will obviously have to organise and plan much less. Travel and accommodation are not necessary. Likewise, you will not have any lost days of arrival and departure.

During the event: The possibilities for networking (e.g. during the conference dinner) are unfortunately very limited. But of course we will try to answer your questions online as well. There will be a Q&A moderator to whom you can write your question anytime. The moderator will then decide if your question should be answered directly or in a Q&A session at the end of each chapter.

Any Questions? Please feel free to contact our events team.

ecSeq Bioinformatics GmbH
Sternwartenstr. 29
D-04103 Leipzig