Virus detection using de-novo assembly - Bioinformatics workshop

Viral infections are considered a significant threat to agricultural production and human health. Effective and accurate detection of viruses in plants and animals is essential for the development of effective strategies to manage the spread and impact of viral diseases.

Conventional virus detection methods, such as ELISA, PCR, hybridization, etc., require prior knowledge or sequence information of potential pathogens, so they are not useful for detecting new viruses or variants thereof. Traditional methods for the detection of unknown viruses, including electron microscopy, are limited in scope and allow only partial characterization of new viruses.

Recently, therefore, Next-Generation sequencing technologies have been intensively used for these purposes as well. They are highly effective in detecting all, including new plant and animal viruses, which is absolutely essential for agricultural production and human health. Probably the most advanced method of this detection is based on the use of shotgun sequencing, subsequent assembly, and virus identification.

Our workshop is focused on this analytical procedure. Upon successful completion of the workshop, you will be able to perform virus detection using de novo assembly of sequences obtained by Next-Generation sequencing methods (the procedure will be demonstrated using a small data set so that it is feasible).

 

What will you learn?

  • How to detect the presence of viruses using de-novo assembly
  • You will gain your own experience with a wide range of bioinformatics tools focused on the analysis of NGS data
  • 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.

 


 

Agenda:

  • De-novo assembly using various algorithms (OLC vs DBG)
  • Genome and transcriptome structure
  • Evaluating assembly
  • Assembly visualization
  • Manipulation with contig sequences
  • Basic Local Alignment Search Tool (Blastn, Blastx)
  • Virus detection using virus database

 


 

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.
  • 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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