• Learn the essential computing skills for everyday NGS bioinformatics
  • Understand key NGS analysis algorithms (e.g., read alignment) and core data formats
  • Use proven bioinformatics tools to process and inspect sequencing data
  • Perform first downstream analyses for studying genetic variation (variant calling, VCF)
  • Compare and apply different approaches for RNA-seq differential expression analysis


Overview

This intensive one-week summer course gives you a deep, practical understanding of Next-Generation Sequencing (NGS) with a strong focus on bioinformatics workflows. You will learn how sequencing technologies influence data quality and downstream interpretation - and how to handle common pitfalls in real datasets.

You will be trained to understand key NGS data formats and identify potential problems and error sources early. Throughout the course, we work with a real-life Illumina RNA-seq dataset.

By the end of the week, you will be able to run essential first analysis tasks independently (QC → mapping → visualization → differential expression) and gain a structured introduction to DNA variant calling. The course is designed for beginners in NGS bioinformatics and welcomes participants with little or no computer science background.

In the evenings, we offer social events such as a conference dinner and a guided city tour through Berlin - great opportunities for networking.

Agenda

  1. Linux for Bioinformatics:
    Learn the essential command-line tools and file formats needed for NGS data analysis, and overcome the first hurdles of working on Linux.
  2. Introduction to NGS data analysis:
    Understand key sequencing methods, terminology, and core analysis steps that apply across many NGS applications.
  3. RNA-seq Data Analyses: Explore RNA-seq alignment strategies and compare approaches for differential expression analysis using real RNA-seq data.
  4. DNA Variant Calling: Learn common variant calling strategies, call your own variants, and discuss real examples together.

Detailed Course Program


Linux for Bioinformatics

  • Introduction to the command line and essential commands for everyday work
  • Combining commands using piping and redirection
  • Introduction to key bioinformatics file formats and databases (e.g., UCSC)
  • Using important bioinformatics toolkits efficiently

Introduction to NGS data analysis

  • Sequencing technologies from a data analyst’s perspective
  • Raw sequencing files (FASTQ format)
  • Preprocessing of raw reads: quality control (FastQC), adapter clipping, quality trimming
  • Read mapping fundamentals (alignment methods, mapping heuristics)
  • Read mapping with common tools (STAR, TOPHAT2)
  • Mapping output (SAM/BAM format)
  • Core NGS toolkits (samtools)
  • Mapping statistics and interpretation
  • Visualization of mapped reads (IGV, UCSC))

RNA-seq Data Analyses

  • Understand split-read mapping
  • Run and compare split-read mappers (TopHat2, STAR)
  • Run pseudo-alignment with Salmon
  • Understand the Tuxedo Suite (cufflinks, cuffcompare, cuffmerge, cuffdiff, etc.)
  • Understand the statistics behind DEseq2 and DIEGO
  • Quantify exons, genes, transcripts
  • Predict
    • Differential splicing using DIEGO
    • Differential gene expression using DEseq2
    • Differential isoform expression using cuffdiff
  • Create extensive diagnostic graphics with R
  • Apply your new skills by working on challenging exercises
NOTE: We will NOT cover single-cell RNA-Seq.

Analysis of genetic variation

  • DNA variant calling: methods and commonly used tools
  • Variant Call Format (VCF): structure, quality fields, and practical interpretation
  • Filtering and annotation of genetic variants

Speakers

Invited Speakers (short talks)

University
t.b.a.

Research Facility
t.b.a.


Your summer school trainers

Dr. Gero Doose
Gero specializes in split-read analysis and downstream interpretation and has published work on circular RNAs in RNA-seq experiments. Publications

Dr. Adam Nunn
Adam is an expert bioinformatician focused on robust pipeline-based analysis across whole-genome DNA-Seq, de novo assemblies, bulk RNA-Seq, and single-cell RNA-Seq Publications

Dr. David Langenberger
David has used NGS since 2006 in multiple large-scale projects (including ICGC) and focuses on practical analysis workflows and interpretation. Publications



Requirements

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.

Included in the Summer School

  •   Course materials
  •   Catering during the workshop
  •   High-performance workstations (no laptop needed)
  •   Conference Dinner
  •   Guided city tour
  •   Networking opportunities
  •   Certificate

Attendance

Location: PC-College, Stresemannstraße 78, 10963 Berlin, Germany
Language: English
Available seats: 30 (first-come, first-served)

Registration Fee: 1,549 EUR (excluding VAT)

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

Travel Information - Berlin

Key dates

Opening Date of Registration: December 9, 2025
Closing Date of Registration: June 12, 2026
Workshop: June 15-19, 2026 (9 am - 5 pm)

Selected feedback from previous Berlin Summer Schools in NGS Data Analysis:

"Excellently structured and polished workshop! The material was challenging but the way it was presented made it easy to follow and fun to engage with. The tutors made the learning environment really friendly and safe, and I got much more out of this workshop than I initially expected. Thank you!" Antonina Karakostova, University of Copenhagen, Denmark

"The course provided an excellent introduction to the analysis of NGS data and covered the most relevant aspects in a well-structured and comprehensible way. The trainers did a really great job guiding us step-by-step through the NGS data analysis workflow and providing theoretical background information and lots of hands-on experience. Overall, a very informative and well-organised course - clear recommendation!" Thomas Wulff, Max Planck Unit for the Science of Pathogens, Germany

The course was dense, well paced, but no stone was left unturned, particularly for statistics and "black boxes", which I particularly enjoyed. Organisation was very good, as well. The wit and expertise of the instructors made this the best such course I have so far attended." Alex Tomazatos, Bernhard Nocht Institute for Tropical Medicine, Germany


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





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

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