De Novo Transcriptome Analysis
Assembly and Differential Gene Expression in Non-Model Organisms

Advance your research. Understand de novo transcriptome assembly and differential gene expression analysis.

In a nutshell

  • Learn the essential computing skills for NGS-based assemblies
  • Understand de novo assembly algorithms and NGS data formats
  • Use de novo assembly tools
  • Find differentially expressed transcripts by using the transcriptome assembly

28 - 30 September 2016
5 - 7 October 2016

Leipzig, Germany

This workshop focusses on the transcriptome assembly and differential gene expression in non-model organisms. While analyses of model organisms generally rely on a reference genome, studies of non-model organisms usually lack this advantage. Thus, the de novo transcriptome analysis in non-model organisms poses some unique challenges.

All workshop attendees will be enabled to perform important first tasks in de novo transcriptome assembly using short-read next-generation sequencing data and uncover differentially expressed genes 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 adapted to the needs of beginners in the field of NGS bioinformatics and comprises this three course modules:

  1. NGS for beginners:
    This module will introduce the essential tools and file formats required for NGS data analysis. It helps to overcome the first hurdles when entering the field of de novo transcriptome assemblies. Different methods of NGS will be explained, the most important notations be given and first analyses be performed.
  2. Introduction to de novo transcriptome assemblies:
    This day covers essential knowledge for the understanding what de novo assemblies are and how they differ from reference based assemblies. You will perform your first assembly and learn how to distinguish between good and bad assemblies.
  3. Using the de novo assembly to find differentially expressed transcripts:
    You will learn how to quantify the transcripts and use it for differential gene expression analysis.

Detailed Course Program

Introduction to NGS data analysis

  • Introduction to the command line and important commands
  • Combining commands by piping and redirection
  • Introduction to bioinformatics file formats (e.g. FASTA, FASTQ)
  • Raw sequence files (FASTQ format)
  • Preprocessing of raw reads: quality control, adapter clipping, quality trimming
  • Visualization of the data quality

Introduction to de novo assembly methods

  • General introduction to assembly methods
  • Differences between de novo and reference based assembly
  • Introduction to de novo transcriptome assembly techniques
  • Introduction to and comparison of tools for de novo transcriptome assembly
  • Performing of first assembly
  • Assessment of transcriptme quality and completeness

Differential gene expression

  • Quantifying assembled transcripts
  • Differential expression analysis (with DESeq)
  • Uncovering biological functions of differentially expressed transcripts


Dr. Alexander Donath (Zoological Research Museum Alexander Koenig)
Alexander is head of section for Computational Genomics at the Zoological Research Museum Alexander Koenig. Since 2011 he is working on NGS data analysis and de novo assembly of non-model organisms. He is involved in a number of large-scale transcriptome and genome research projects, for example 1KITE and i5k. more

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.

Dr. Christian Otto (CCR Bio-IT)
Christian is one of the developers of the read mapping tool segemehl and is an expert on implementing efficient algorithms for HTS data analyses.


  • 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: iad Pc-Pool, Rosa-Luxemburg-Stra├če 23, Leipzig, Germany
Language: English
Available seats: 24 (first-come, first-served)

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

Travel Information - Leipzig

Key dates

Opening Date of Registration: 1 March 2016
Closing Date of Registration: 1 September 2016
Workshop: 28 - 30 September 2016 (8 am - 5 pm)
Workshop: 5 - 7 October 2016 (8 am - 5 pm)


"Good resume of the last technologies and applications. Definitly will improve the comunication with our bioinformatics colleagues for perfom the proper analysis and understanding of the data. Thanks for an intensive but nice course." Susana Gonzalez Fernandez-Nino, Bayer Crop Science, Germany

"Very valuable workshop which improved my bioinformatics understanding a lot and provided interesting aspects, I will put more focus on while analyzing our own data." Corinna Streitner, KWS Saat AG, Germany

"Excellently prepared and performed workshop. A lot of information provided." Jakub Mrazek, Czech Academy of Sciences, Czech Republic

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