• Learn the essential computing skills for NGS bioinformatics
  • Understand NGS analysis algorithms (e.g. read alignment) and data formats
  • Use bioinformatics tools for handling NGS data
  • Perform first downstream analyses for studying genetic variation
  • Compare different approaches for differential expression analysis

The purpose of this intense one week summer course is to get a deep 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. You will be trained on understanding NGS data formats and handling potential problems/errors therein.

All students will be enabled to perform important first tasks of NGS data analysis themselves. The layout of the summer school has been adapted to the needs of absolute 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.

In the evenings there will be social events, like a conference dinner, or a guided city tour through Berlin. These are always great networking possibilities for the participants.

Read our detailed course program.

  1. Linux for Bioinformatics:
    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.
  2. Introduction to NGS data analysis:
    Different methods of NGS will be explained, the most important notations be given and first analyses be performed. This course covers essential knowledge for analysing data of many different NGS applications.
  3. DNA Variant Calling: In this module different bioinformatics tools for variant calling will be described. We then apply various methods for variant calling and filtering using DNA-Seq data.
  4. RNA-seq Data Analyses: In this module different bioinformatics tools for RNA-seq alignment will be described and tested. We then apply and compare the various approaches for differential expression analysis using RNA-Seq.

Detailed Course Program

Linux for Bioinformatics

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

Introduction to NGS data analysis

  • Introduction to sequencing technologies from a data analysts view
  • 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)

Analysis of genetic variation

  • DNA variant calling
  • Filtering of genetic variants

RNA-seq Data Analyses

  • Understand split-read mapping
  • Run different split-read mappers (tophat, segemehl, STAR)
  • Understand the Tuxedo Suite (cufflinks, cuffcompare, cuffmerge, cuffdiff, etc.)
  • Predict new transcripts/isoforms using cufflinks/cuffmerge
  • Quantify exons/genes/transcripts
  • Predict
    • Differential exon usage using DEXseq
    • Differential gene expression using DEseq
    • Differential isoform expression using cuffdiff

Invited Speakers (short talks)

  • Dr. Anaïs Le Rhun (MPI for Infection Biology; Emmanuelle Charpentier's group)
  • Dr. Dominic Rose (Roche Diagnostics Deutschland GmbH)
  • Dr. Alexander Ullrich (Robert Koch-Institut)

Your summer school trainers

Dr. Gero Doose (ecSeq Bioinformatics)
Gero found and published several circularized RNAs in various RNA-Seq experiments. He specialized on split-read analysis some years ago and has a strong expertise in downstream analyses. Publications

Dr. Christian Otto (Seamless NGS)
Christian is one of the developers of the read mapping tool segemehl and is an expert on implementing efficient algorithms for NGS data analyses. Publications

Dr. David Langenberger (ecSeq Bioinformatics)
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. Mario Fasold (Seamless NGS)
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. Publications


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.

A basic knowledge of Linux & Bioinformatics (commandline usage, common commands and tools) is beneficial, but not required. You could prepare yourself with the Learning the Shell Tutorial.

  •   Course materials
  •   Catering during the workshop
  •   High-performance workstations (no laptop needed)
  •   USB-Stick for taking home results and analysis
  •   Conference Dinner
  •   Guided city tour
  •   Networking opportunities


Location: PC-College, Stresemannstraße 78, 10963 Berlin, Germany
Language: English
Available seats: 25 (first-come, first-served)

Registration Fee: 1,390 EUR (excluding VAT)

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

Travel Information - Berlin

Key dates

Opening Date of Registration: 1 February 2017
Closing Date of Registration: 1 September 2017
Workshop: 11 - 15 September 2017 (9 am - 6 pm)


"There are too many things to consider when using NGS technology. I really needed a course like this to get started with a proper analysis of my own data. " Lisa Kutsche, Center for Regenerative Therapies Dresden, Germany

"As someone who was previously terrified of the command line, this was a terrific course to build confidence in navigating the terminal. Moreover, I walked away with a much deeper understanding of sequencing chemistry and the relative merits of different software packages for analysing different types of sequencing data. I highly recommend this course for any wet lab biologist whether at the student, postdoc, or PI level!" Alexandra McCorkindale, Max Delbrück Center for Molecular Medicine, Germany

"This was a very intensive course, which gave tremendous help to anyone trying to work with NGS data. Difficult concepts were very effectively simplified and explained. Should be a great help in anyone interested in NGS." Tamas Varga, University of Debrecen, Hungary

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

ecSeq Bioinformatics GmbH
Sternwartenstr. 29
D-04103 Leipzig
Email: events@ecSeq.com