Workshop: Oxford Nanopore long reads - de novo assembly

Oxford Nanopore technology provides a novel amplification-free approach to DNA sequencing that yields long and label-free reads. This technology quite obviously presents cost-effective and fast solution for various applications including de novo whole genome sequencing of even complex genomes. On the other hand, it differs in many aspects from Illumina short-read sequencing technology and requires not only dedicated equipment and chemistry but also specific software tools and algorithms including basecallers, assemblers and post-assembly correction tools.

Additionally, Nanopore instruments are cheap and small which makes them easy to acquire not only in labs of sequencing providers like our company or academic core facilities but also in many research labs directly. Researchers may easily learn to use this instrumentation in order to produce data but at the same time may run into trouble when analyzing them since tools and algorithms used are application and sequencing platform specific.

Our 2-day workshop aims at researchers wishing to learn more about handling of Oxford Nanopore long reads with a special focus on de novo assembly pipeline. On the first day, you will be briefly introduced into the Linux system and Nanopore technology and on the second day you will perform your own de novo assembly using provided data sets.

Various Oxford Nanopore specific tools and algorithms will be presented including but not limited to Miniasm and Canu assemblers, Racon correction tool and others. A detailed theoretical session always precedes a hands-on session. All workshop participants will perform all data analysis tasks themselves!


Who should attend?

This workshop is for beginners as well as advanced users, life scientists and bioinformaticians interested in Oxford Nanopore long reads technology. No prior knowledge of sequences data analysis or specific programming skills are required.

What what will you get?

  • At the last day of the workshop you will be provided with a bootable USB stick with all tools used and data analyzed
  • All your 2-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
  • The powerful computer infrastructure available at the conference center will be used (no personal laptops are required/allowed)



Workshop agenda

Day 1: Linux as a tool for scientists - Go beyond the graphical interface

  • Introduction to the NGS data analysis
  • Linux system as a tool for data analysis
  • Basic linux commands for beginners
  • Introduction to Oxford Nanopore technology

Day 2: De novo assembly of long reads - A different approach

  • Assembly of MinION reads
  • Pre-assembly correction tools
  • Post-assembly correction tools
  • Evaluating assembly
  • Assembly visualization




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, Bioinformatician, SEQme
  • Jan Pačes, Bioinformatician, Institute of Molecular Genetics
  • Štěpán Stočes, Bioinformatician, SEQme
  • Petr Vácha, NGS Application specialist, SEQme


Workshop Logistics

  • Language: English
  • Registration fee includes: Workshop materials, Lunches/Coffee breaks
  • How to reach the Workshop venue
  • 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 Workshop.





A basic knowledge of BASH and Unix terminal 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.

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