Illumina technology in your daily routine - Workshop

Next-Generation sequencing (NGS) technologies play an increasingly important role in all areas of science, research and diagnostics. In particular, Illumina's technology today represents a key part of the work of any routine diagnostic or research laboratory focused on DNA sequencing.

This technology generates huge volumes of data, the processing of which requires, although it is often not presented, expert knowledge in the use of the Illumina BaseSpace Sequence Hub and in the subsequent relatively standardized analysis of the raw data, which is usually followed by a very specific pipeline taking into account the specific application.

There are many commercial software packages that reflect the different needs of technology users and their requirements for the final processing of results and try to make certain steps of this process easier for them, but this often leads to the paradoxical situation of "use without understanding". The selected applications then require knowledge of specific procedures for data processing – for these purposes, we refer to our workshops focused on e.g. mutation detection (variant calling), RNASeq, microbiome analysis, etc.

However, basically all users of Illumina technology need to work with BaseSpace Sequence Hub for basic data processing from their instruments and also use selected downstream tools for data quality control, for example.

Our workshop Illumina technology in your daily routine will allow you to get to know in detail how Illumina technology generates data and how to control its quality. The goal of the workshop is to teach you how to use the BaseSpace Sequence Hub and then walk you through the routine data analysis steps performed before moving on to the subsequent application-specific steps of the process. The outcome of our three-day workshop should be your ability to evaluate the quality of a dataset generated by Illumina sequencers and clean that dataset to obtain a high-quality dataset. Which is a significant difference.


Who should attend?

  • The workshop is especially suitable (not only) for users of Illumina devices, for example device operators from diagnostic laboratories, for whom easy use of not only the tools provided by the manufacturer and fast data processing leading to quality outputs are essential in their daily routine.
  • Furthermore, it is extremely suitable, for example, for application or sales specialists from companies that supply NGS-based diagnostic kits and from whom their clients - diagnostic laboratory staff - expect help and support in their use.
  • Last but not least, it is also intended for all other people interested in the mentioned technology.

So the event is for you if you are:

  • Laboratory workers – biologists and/or bioinformaticians interested in or performing DNA sequencing using Illumina technology in diagnostic and research laboratories.
  • Support staff, e.g. specialists from companies dealing with the supply of NGS-based diagnostic kits, library creation kits, etc.
  • The workshop is also suitable for beginners, no previous experience with NGS technologies is necessary.
  • If you have absolutely no knowledge of NGS, even terminology, we recommend that you consider attending our Introduction to Next Generation Sequencing course.
  • Feel free to contact us if in doubt.


  • A computer literacy and basic knowledge of molecular biology.
  • Knowledge of BASH and the terminal is not required, but is an advantage. We recommend going through one of the freely available guides, eg at this link.

What will you learn?

  • You will learn the principles of Illumina sequencing technology and the BaseSpace Sequence Hub interface.
  • You will get a complete description of the most common NGS data formats and their use in subsequent data analysis.
  • After this three-day workshop, you will be able to professionally evaluate sequencing results and verify data quality, including the removal of low-quality and unwanted data, e.g. contamination.
  • You will have the opportunity to interact with experienced speakers and other participants.




  • NGS technologies and their outputs
  • Overview of NGS data formats (fasta, fastq, SAM/BAM, VCF, GFF3)
  • Unix and how to use it in (not only) data analysis
  • Controlling your PC using the Terminal
  • Preparing Illumina sequencing libraries – theory, tips and tricks
  • Best practice – loading the flowcell, understanding the sample sheet, PhiX control
  • Introduction to Illumina BaseSpace
  • Raw NGS data quality check using fastQC and MultiQC
  • Pre-processing of short-reads / FASTA/FASTQ files
  • Read mapping to the reference sequence (BWA)
  • Visualization and evaluation of mapping quality (IGV, Qualimap2)




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?

  • This is a workshop combining lectures and practical exercises. You will perform data analysis yourself on the provided computers under the supervision of experienced instructors.
  • On the last day of the workshop, you will receive a bootable USB disk on which all the tools used and all the data analyzed by you will be stored. You take your three days' worth of work with you and can follow up on it whenever you return to your lab!

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.

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