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 choose and accomplish the most appropriate approach to analyze taxonomic composition of your metagenomics / microbiomics data
- How to process data from raw sequence to the application of selected algorithms for analyzing 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…
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.
- Ondřej Lukšan, NGS Lab specialist
- Štěpán Stočes, Bioinformatician
- Petr Vácha, NGS Application specialist
- Tomáš Větrovský, Bioinformatician
- Language: English
- Registration fee includes: Workshop materials, Lunches/Coffee breaks
- Events: Budweiser Budvar Guided Brewery Tour + Conference dinner (both also included in the registration fee)
- How to reach the Workshop venue - the city of Ceske Budejovice (in the southern part of the Czech Republic) can be easily accessed by car/bus/train from various directions. Please let us know should you need help with your travel arrangements.
- 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.
To sign up for the workshop you must be registered on our website - if you have not registered yet please proceed using this link, then get back here and click the Sign up button below.