Next-Generation Sequencing data analysis – Workshop for beginners!

22. - 24.5.2019 08:30 - 17:00 Brno, CZECH REPUBLIC 750 € without VAT English Seats available: 0

Nowadays, Next-Generation sequencing technologies form an essential part of almost all disciplines of biological sciences in research and diagnostics. Due to their quantity and namely complexity, NGS data are typically processed by qualified bioinformaticians or computational biologists. This presents a serious issue even for experienced researchers who have never studied this field of science simply because it has emerged just recently and suddenly there is a need to adapt to completely new tools, workflows and scientific terminology not to perform this sequencing data analysis process – after all, this is why we employ bioinformaticians, but to understand it properly.

Our workshop gives you the opportunity to understand basics of NGS data processing. The aim of the workshop is to teach you to perform basic steps of NGS data analysis including but not limited to raw data manipulations, quality control, removal of low-quality sequences, sequencing adapters, artifacts, or other contaminations, and especially preparation of a high-quality data set that can be used for downstream analysis.

You will get to know various NGS data formats, learn about specific problems of sequencing technologies used and how to handle them, and understand the background of individual processes in NGS data editing. You will not become a bioinformatician after this 3-day workshop, but you will set off for becoming a qualified partner for bioinformaticians in your team.

Please note: If you are not familiar with Next-Generation sequencing technologies, we do encourage you to take part also at our 2-day Introduction to Next-Generation Sequencing Course, which is just preceding this workshop.

 

Who should attend?

This workshop is designed for biologists or beginners in bioinformatics who perform or plan to perform Next-Generation sequencing data analysis. No prior knowledge of sequence data analysis or specific programming skills are required.

 

You will learn to:

  • Work in a command line in Ubuntu Unix operating system environment
  • Evaluate quality of raw NGS data
  • Perform basic operations with NGS data
  • Remove low-quality reads, sequencing artifacts, duplications and contaminations
  • Visualize results
  • You will have the option of networking with experienced team of speakers and other participants

Overall, you will learn all essential steps how to prepare NGS data for advanced downstream analysis (application-specific).

 

And what will you get?

  • At the last day of the week you will be provided with a bootable USB stick with all tools used and data analyzed
  • All your 3-day work stored and ready to be used immediately when you get back to your lab!

 

During the workshop…

  • Trainers will provide lectures with follow-up hands-on exercises in order to have the participants learning and assessing their knowledge
  • All workshop participants will perform all steps of data analysis tasks themselves!
  • The powerful computer infrastructure available at the conference center will be used (no personal laptops are required/allowed)

Overall, get ready for a very intensive workshop…

 


 

Workshop agenda:

Day 1: Unix and how do I use it? - Get to know the environment

  • General introduction to NGS data
  • Overview of NGS data formats
  • Introduction to the Linux system
  • Navigation and basic commands in the Terminal

Day 2: NGS data quality control Was my sequencing successfull?

  • Standard commands in the Terminal to process NGS data
  • Visualization of the quality of raw NGS data
  • Pre-processing of short-reads FASTA/FASTQ files using various programs

Day 3: How do I get high quality NGS data set? - Get the best out of it!

  • Read mapping to the reference sequence
  • Visualization and evaluation of mapping quality
  • Identification and removal of duplicate reads
  • Identification of unmapped reads – Blast
  • ...

 


 

Speakers

Our team of speakers includes professionals focusing on data analysis but also sample processing in Next-Generation Sequencing lab and other related tasks and therefore as a team able to provide a comprehensive insight into the whole data analysis workflow in context.

  • Pavlína Kočová, Bioinformatcian
  • Štěpán Stočes, Bioinformatcian
  • Petr Vácha, NGS Application specialist

 

Course Logistics:

  • Language: English
  • Registration fee includes: Workshop materials, Lunches/Coffee breaks
  • How to reach the Workshop venue - the city of Brno (in the eastern part of the Czech Republic) can be easily accessed by car/bus/train from various directions. Please let us know should you need help with your travel arrangements.
  • Please kindly notice that lodging, travel and other incidental expenses are the responsibility of the attendee and that no labwork is to be performed during the course.

 

Download

 

Resources:

A basic knowledge of BASH and Unix terminal usage are not necessary but advantageous. If you are a newbie to the field, we recommend you go through some tutorials – please follow for example this link.

 


Next-Generation Sequencing data analysis – Workshop for beginners!

When: 22. - 24.5.2019
Time: 08:30 - 17:00
Where: Brno, CZECH REPUBLIC
Address: JIC INBIT, Kamenice 34, Brno
Price: 750 € without VAT
Language: English
Seats available: 0
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