Microbiome and Metagenome Data analysis workshop

This workshop covers microbiomics / metagenomics analysis from quality control, filtering and assembly/clustering to taxonomic classification, functional assignment and comparative metagenomics. 
Both community analysis of amplicon sequencing data as well as analysis of whole genome shotgun sequencing data will be covered including methods for statistical comparisons of multiple metagenomic samples.

You will be briefly introduced into the Linux operating system and in this environment you will analyze sequencing data using various publicly available tools.


Who should attend?

This workshop is aimed at life scientists and bioinformaticians working or being interested in the field of metagenomics / microbiomics. No prior knowledge of metagenomic / microbiomics sequences analysis or specific programming skills are required. 


What will you learn?

  • How to select and use the most appropriate approach for analysis of taxonomic composition of your metagenomics / microbiomics samples
  • How to process data from raw sequences and apply specific algorithms for analysis of metagenomic datasets
  • You will gain hands-on experience using a range of data resources and tools
  • You will have the option of networking with experienced team of speakers and other participants

And what will you get?

  • At the last day of the week you will be provided with a bootable USB stick with all tools used and data analyzed
  • All your 5-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
  • All workshop participants will perform all steps of data analysis tasks themselves!
  • The powerful computer infrastructure available at the conference center will be used (no personal laptops are required/allowed)
  • Overall, get ready for a very intensive week…



Workshop agenda:

Day 1: Linux as a scientific tool - Get to know the environment

  • General introduction to data analysis
  • Introduction to the Linux system
  • Basic commands in Terminal and their practical use
  • Overview of common data formats

Day 2: Basic operations with NGS data Get a full picture of NGS workflow

  • Current NGS technologies
  • Quality control of sequence data
  • Editing sequences in various programs
  • Introduction to alignment

Day 3: Read mapping and alignment visualization - The must-have skills

  • Read mapping
  • Quality control of alignment sequencing data
  • Alignment visualization

Day 4: 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

Day 5: 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




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
  • Štěpán Stočes, Bioinformatician
  • Petr Vácha, NGS Application specialist
  • Tomáš Větrovský, Bioinformatician


Workshop Logistics

  • Language: English
  • Registration fee includes: Workshop materials, Lunches/Coffee breaks
  • Conference dinner (included in the registration fee)
  • 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 usage 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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