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

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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 for studying genetic variation

When?
September 2 - 4, 2024

Where?
Munich, Germany

52 votes

Scope and Topics

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 new and fast evolving research topic.

Check our new course layout.

Our Philosophy

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.

Workshop Design

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
  • 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 (IGV, UCSC)
  • DNA variant calling
  • Variant Call File Format (VCF)
  • Filtering DNA variants

Speakers

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).

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.

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.

A basic knowledge of Linux & Bioinformatics (commandline usage, common commands and tools) is beneficial, but not required.

Included in the Course

  •   Course materials
  •   Catering during the workshop
  •   Conference dinner
  •   High-performance workstations (no laptop needed)
  •   Downloadable environment for seamless continuation / repetition after the course
  •   Certificate

Attendance

Location: cmt GmbH, Hansastraße 32, 80686 München, Germany
Language: English
Available seats: 20 (first-come, first-served)

Registration Fee: 989 EUR (excluding VAT)

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

Travel Information - Munich

Key dates

Opening Date of Registration: December 13, 2023
Closing Date of Registration: August 24, 2024
Workshop: September 2 - 4, 2024 (9 am - 5 pm)

What our participants are saying

"Very informative workshop with well explained lectures and exercises. It covers different aspects of NGS, which are all needed to perform meaningful and high-quality data analysis. A great plus is that the virtual machine used in the course can be downloaded, so all tools can easily be used also afterwards, with one's own data (without the need to install them)." Jelena Ivancic Jelecki, University of Zagreb, Croatia

"A very comprehensive insight into the standard analysis workflow for processing NGS data just by using the Linux command line and common open source toolkits. The instructors have many years of expertise in their field, actively involve the participants in the discussion and fully address all questions. All in all, a very enjoyable course that I can highly recommend to anyone who wants to gain an understanding of bioinformatics analysis of NGS data." Marian Rosenstengel, LABCON-OWL, Germany

"For a 3-day course, it covers all aspects one needs to reflect on & start-up their own analysis. The explanations on quality control, alignment, mapping and eventually: variant calling, were enlightening. Each of these topics was covered piece by piece, with attention to questions and a limited background in bioinformatics. It gave us the opportunity get familiar with the Linux command-line, which was thoroughly explained and put to practice with exercises on template data." Mathijs Mutsaers, Institute of Tropical Medicine, Belgium

See all course reviews

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