Next-Generation Sequencing – Workshop, NGS Data Analysis: A Practical Introduction, Quality Control, Read Mapping, Visualization, and DNA Variant Analysis.
March 25 – 27, 2020
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
Scope and Topics
The purpose of this workshop is to get a deeper understanding of Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. The advantages and disadvantages of current sequencing technologies and their implications for 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 the 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 an optimal learning experience, we carefully prepare our learning materials and example data. All materials, tools, and results created during the course are for taking home with you.
This workshop has been redesigned and adapted to the needs of beginners in the field of NGS bioinformatics and comprises these three-course modules:
- 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 of various applications will be given.
- 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.
- Introduction to NGS data analysis:
Important first NGS analysis tasks will be explained and performed. This module covers essential knowledge for analyzing data of different NGS applications.
- Introduction to sequencing technologies from a data analysts view
- Common NGS data analysis issues
- Applications of sequencing technologies
- Notations and NGS Terminology
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 to analyze sequencing data of several large consortium projects.
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.
Basic knowledge of Linux & Bioinformatics (command line usage, common commands, and tools) is beneficial, but not required.
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
Included in the Course
- 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, Hansastraße 32, 80686 München, Germany
Available seats: 20 (first-come, first-served)
Registration Fee: 949 EUR (excluding VAT)
Travel expenses and accommodation are not covered by the registration fee. Travel Information – Munich
Opening Date of Registration: November 14, 2019
Closing Date of Registration: March 1, 2020
Workshop: March 25 – 27, 2020 (9 am – 5 pm)
Any Questions? Please feel free to contact the events team.
ecSeq Bioinformatics GmbH
To register click here: https://www.ecseq.com/workshops/register
Next-Generation Sequencing – Workshop
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