91AV

Today, Next-Generation sequencing technologies (NGS) are an essential part of almost all life sciences research and diagnostics. Due to their quantity and especially their complexity, NGS data are typically processed by qualified bioinformaticians. This is also a serious problem for experienced professionals in life sciences who have never studied NGS, simply because it is too fresh, and suddenly need to adapt to completely new tools, workflows and scientific terminology, not to analyze NGS data themselves - after all, that is why we have bioinformaticians, but to be able to ask the right questions and understand the results.

Our workshop will allow you to understand the basics of NGS data processing. Its goal is to learn to perform the basic steps of NGS data analysis, including manipulation of raw data, quality control, removal of low quality sequences, sequence adapters, artifacts or other contamination. The result should be a perfect mastery of the process, the output of which is a set of high quality data that can be used for subsequent analysis.

You will get acquainted with various formats of NGS data, you will learn about specific advantages and disadvantages of used sequencing technologies and how to deal with them, and you will understand the background of individual processes used to modify NGS data. After this three-day workshop, you will not become a bioinformatician, but you will be well on your way to becoming a qualified partner for bioinformaticians in your team.

Who should attend?

• The event is intended for biologists or bioinformaticians interested in analyzing the results of Next-Generation sequencing. It is perfectly suitable for complete beginners in the field of data analysis, no previous experience with sequencing data analysis is required.
• A necessary prerequisite is computer literacy and basic knowledge of molecular biology (DNA, RNA, gene expression, PCR). Knowledge of BASH and the terminal is not required, but is an advantage. We recommend going through one of the freely available guides.
• If you already have some experience in NGS data analysis and want to revive and possibly deepen it (regardless of the specific procedures for a particular NGS application), this event is also for you.
• If, on the other hand, you have no knowledge of NGS at all, we recommend that you first take the theoretical Introduction to Next-Generation Sequencing course.
• If in doubt, do not hesitate to contact us.

What will you learn?

• How to work in Ubuntu command line
• How to evaluate the quality of raw NGS data
• How to perform basic operations with NGS data
• How to remove sequencing reads with low quality, artifacts, duplication and contamination
• How to view results
• You will have the opportunity to communicate with an experienced team of speakers and other participants

In summary, you will learn all the basic steps of preparing NGS data for subsequent bioinformatics processing, which is already specific to a particular application.

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: 
The team of lecturers is composed of professionals, employees of SEQme and possibly invited guests - experts on the topic, who have long been using various Next-Generation sequencing technologies. They focus not only on data analysis, but also on laboratory processing of samples in the NGS laboratory, design of NGS projects and other related tasks and are therefore able to provide a comprehensive insight into the whole issue in context.

Event details: 

• Trainers always explain the topics using presentations, but the main emphasis is on subsequent practical demonstrations so that all participants actively learn to use the explained procedures and tools
• All participants themselves perform important steps of NGS data analysis, each has their own computer!
• We use powerful computers, which are provided to all participants of the event. Using your own computers and / or data files is not possible.

Event logistics:

• Language: English
• The registration fee includes printed presentations for the course / workshop, lunches and refreshments.
• Lodging, travel and other incidental expenses are the responsibility of the attendee.
• Please note that no laboratory experiments are performed during the event.

Special offer: All our courses and workshops can also be organized at your workplace, for your working group. So as a tailor-made event. Some of our events were even created in this way - at the client's request. The advantage of this format is, of course, the ability to prepare a turnkey event for your team, reflect your specific requirements and needs, including the ability to work with your data. If you are interested, do not hesitate to contact us.