Metataxonomics and metagenomics – Bioinformatics workshop

Metagenomics is the study of genetic material obtained directly from environmental samples. This is useful when trying to understand what microbes are present in a sample and what they do in a particular environment.

The traditional procedure was to collect the sample, cultivate it and identify it. This approach is very lossy, the main limitation of course is that you can only work with what is growing. However, the vast majority of microbes cannot be cultivated and if they do not grow, then they cannot be subsequently identified.

Current NGS-based technology allows us to completely bypass the culture step and instead extract nucleic acids directly from the sample, allowing access to theoretically 100% of the genetic content in the sample. So it allows us to answer two basic questions that are asked in every metagenomics project: Who is there and what is he doing there?

In metagenomic projects, two fundamental approaches are applied - sequencing of amplicons, obtained by amplification of suitable target regions, and shotgun sequencing. Each approach has its advantages and disadvantages. Amplicon sequencing is easier, cheaper and less reliable in terms of identification, it can only answer the question "Who's there?". Shotgun sequencing, on the other hand, is more complex and undoubtedly more expensive, but it also adds value in the form of an answer to the question "What does it do there?".

Our metagenomic workshop is typically but not necessarily designed as a two-day. On the first day you will analyze the data obtained by sequencing amplicons (metataxonomics), on the second day by shotgun sequencing (metagenomics) including methods of statistical comparison of metagenomic samples. You will process data from quality control, filtering, assembly / clustering to taxonomic classification, functional classification, and comparative metagenomics.

 

What will you learn?

  • You will learn how to select and choose the most suitable procedure for taxonomic analysis of your metagenomic data
  • You will learn how to process data, starting with raw data (reads) to the use of selected algorithms for the analysis of metagenomic data
  • You will gain your own experience with a wide range of bioinformatics tools focused on the analysis of NGS data, including advanced statistical tools
  • 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:

  • Metataxonomic analysis – The Amplicon Session
    • Amplicon sequencing of marker genes
    • Analysis of marker genes – practical part
      • Data preparation (sequence trimming, quality filtering, OTU clustering)
      • OTU table construction and OTUs classification
    • Evaluation of results from metataxonomic analysis
  • Metagenomic analysis – The Shotgun Session
    • Metagenome data processing and de novo assembly
    • Analysis of metagenomics data – practical part
      • Data preparation (adaptor trimming, quality filtering, digital normalization)
      • Annotation of contigs (MG-RAST)
      • Mapping reads to contigs (gene coverage/quantification, sample comparison)
      • Binning (MaxBin2)
      • Evaluation of results from metagenomic analysis

 


 

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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