De novo assembly – Bioinformatics workshop

Why should you join? This is why!


The dominant sequencing technology on the market has long been Illumina's short read technology. One of the applications where this dominance is a bit of a problem and, on the contrary, creates new opportunities, is the assembly of genomes, especially de novo assembly.

Newer sequencing technologies (especially Pacific Biosciences and Oxford Nanopore) provide significantly longer sequencing reads, which is crucial for successful assembly. On the other hand, they differ from the market-leading Illumina technology and require not only specialized equipment and reagents, but also specific software tools and algorithms, including basecallers, assemblers, and assembly correction tools.

Oxford Nanopore sequencers are (unlike PacBio instruments) cheap and small instruments, which makes it easier to acquire them not only in the laboratories of sequencing service providers, such as our company or academic core facilities, but also in many research laboratories directly. Researchers can easily learn how to use these devices to generate sequencing data, but they can also encounter problems in analyzing this data because the tools and algorithms used are specific to this sequencing platform.

Our workshop is aimed at scientists who want to learn more about working with data obtained using Oxford Nanopore with a special focus on hybrid de novo assembly using Illumina + Oxford Nanopore reads. During the workshop, you will independently perform your own de novo assembly using the provided data files.


What will you learn?

  • You will be introduced to various Oxford Nanopore tools and algorithms, Flye, SPAdes and Canu assemblers, Pilon repair tool, etc.
  • You will learn not only to perform your own assembly, but also to check the correctness and perform correction of the output
  • You will have the opportunity to communicate with an experienced team of speakers and other participants


Who should attend?

  • The event is intended for up to 10 participants, 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.




  • Technological overview
  • Raw data preprocessing
  • Assembly of Illumina reads
  • Assembly of MinION reads
  • Hybrid assembly of Illumina and MinION reads
  • Post-assembly correction tools
  • Evaluating assembly
  • Assembly visualization
  • Assembly annotation




  • 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 is assigned a powerful computer!
  • Since 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.
  • Using your own data files is not possible.


Event logistics:

  • Language: English
  • The registration fee includes presentations in electronic form.


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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