Next-Generation Sequencing Data Analysis: A Practical Introduction
Quality Control, Read Mapping, Visualization and Differential Expression Analysis

Advance your research. Understand NGS and analyze sequenced 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 and find differentially expressed genes

7 - 9 December 2016

Munich, Germany

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 (differential gene expression). In the course we will use a real-life RNA-seq 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 new and fast evolving research topic.

Check our new course layout.

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. All materials, tools and results created during the course are for take home with you.

This workshop has been redesigned and 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
  • Cobining 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, UCSCtools)

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, Bowtie2, STAR, segemehl)
  • Mapping output (SAM/BAM format)
  • Usage of important NGS toolkits (samtools, BEDtools)
  • Mapping statistics
  • Visualization of mapped reads (IGV, UCSC)
  • Differential expression analysis (with DESeq)


Dr. David Langenberger (ecSeq Bioinformatics)
David started working with small non-coding RNAs in 2006. Since 2009 he uses NGS technolgies 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).

Dr. Mario Fasold (CCR Bio-IT)
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 sequecing data of several large consortium projects.


  • basic understanding of molecular biology (DNA, RNA, gene expression, PCR, ...)
  • For the Introduction to NGS Data Analysis and downstream courses: basic linux & bioinformatics knowledge (shell usage, common commands and tools). You should be familiar with the commands covered in the Learning the Shell Tutorial

The target audience is biologists or data analysts with no or little experience in analyzing RNA-Seq data.

  •   Course materials
  •   Catering during the workshop
  •   Conference dinner
  •   High-performance workstations (no laptop needed)
  •   USB-Stick for taking home results and analysis


Location: cmt GmbH, Hansastra├če 32, 80686 M├╝nchen, Germany
Language: English
Available seats: 20 (first-come, first-served)

Travel expenses and accommodation are not covered by the registration fee.

Travel Information - Munich

Key dates

Opening Date of Registration: 1 July 2016
Closing Date of Registration: 1 November 2016
Workshop: 7 - 9 December 2016 (9 am - 5 pm)


"Since just having a little experience in analyzing RNA-Seq data, my knowledge about the unix environment, mapping tools and downstream analyses improved a lot during the workshop. With the help of the provided workshop materials it was quite easy to follow the excellent speakers. Several exercises supported the learning process as well." Alexander Nolze, Martin-Luther-University Halle-Wittenberg, Germany

"The ecSeq workshop on 'Next-Generation Sequencing Data Analysis' was very informative. I have no doubt that I acquired new skills, thus, extended my knowledge of analyzing the big data. I am integrating most of these in my current research analyses. Thank you ecSeq Bioinformatics Team!" Harris Onywera, Center for Genomic Regulation, Spain

"This ecSeq course provided a very good 3-day intensive workshop on NGS, Analysis, and BASH to give anyone working with genetic material a good foundation to expand their research project in a number of cutting edge directions. The instructors are warm and knowledgeable and eager to help anyone sincerely interested in learning these techniques." Trevor Burt, ZFMK (Koenig Museum), Germany

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

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

ecSeq GmbH
Brandvorwerkstr. 43
04275 Leipzig