Variant calling and annotation – Bioinformatics workshop

High-throughput sequencing (or Next-Generation sequencing - NGS) is nowadays a common part of research and diagnostics. It provides a range of highly variable outputs depending on the application. One of the most common requirements for the use of NGS is the accurate identification of diagnostic, prognostic and predictive determinants.

Key determinants are single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels). Their detection and identification - so-called variant calling in sequencing data is in principle a simple matter, which in practice is far from simple and the distinction between real variant (mutation) and experimental error requires sophisticated computational and / or heuristic techniques.

In our workshop you will learn exactly these procedures. It includes practical demonstrations of procedures that deal with all steps of this process, starting with editing the raw sequencing data and ending with the identification and annotation of individual variants.

The workshop will guide you through data quality control, filtering, mapping, identification of variants, their annotations and statistical processing. After its completion, you will be able to use this bioinformatics procedure in your own practice.


What will you learn?

  • To process raw sequencing data (reads)
  • How to work with a reference sequence
  • You will be able to map the sequencing reads to the reference sequence and remove PCR duplicates
  • You will learn to identify, filter, annotate and evaluate genomic variants (SNPs and indels)
  • You will gain your own experience with a number of specific bioinformatics tools focused on analysis of this type
  • You will have the opportunity to communicate with an experienced team of speakers and other participants


Who should attend?

  • The event is intended for advanced applicants, biologists or bioinformaticians interested in this specific area of data analysis.
  • Knowledge of BASH and the terminal is a prerequisite. If you have no experience with the analysis of sequencing data, we recommend that you first complete the more general Next-Generation Sequencing data analysis – Workshop for beginners to learn the basics.
  • If in doubt, do not hesitate to contact us.




  • Quality control of sequencing reads
  • Removal of low quality and spurious sequences
  • Mapping of individual sequences to a reference genome
  • De-duplication of mapped sequences
  • Variant calling
  • Genomic variant annotations and functional effect prediction




  • 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.
  • SEQme is not an official distributor of any NGS technology company (Illumina, IonTorrent, PacBio, OxfordNanopore, etc.). We are users, just like you. In our sequencing laboratories, we always use the most suitable technologies from various manufacturers, always with the aim of maximum effect for your sequencing projects. We then share the knowledge gained in this way with the participants of our courses and workshops.


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.
  • If it is an online workshop, you will need your own computer with an Internet connection - you will remotely connect to our powerful analytical computers. There are no special demands on your computer, it is important to have admin rights to install one or two software packages to enable the connection. Simple instructions on how to connect to our workstations will be provided to registered participants well in advance of the event. We recommend that you have headphones to communicate with our lecturers and consider having two monitors - sometimes it is necessary to have multiple windows open at once and having two monitors is comfortable.


Event logistics:

  • Language: English
  • The registration fee includes printed presentations for the course / workshop (for online events, presentations are provided exclusively in electronic form). If this is the „physical“ event (i.e. this is not an online workshop), the price also includes 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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