Who should attend?
This workshop is aimed at beginners as well as advanced users, life scientists and bioinformaticians interested in the analysis of Next-Generation sequencing data. No prior knowledge of sequences data analysis or specific programming skills are required.
What will you learn?
- How to perform basic manipulations with raw sequences and read mapping
- How to choose and accomplish the most appropriate approach to de novo assembly and how to evaluate its outcome
- How to identify and annotate variants by using the Genome Analysis Toolkit
- 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 - Go beyond the graphical user interface!
- General introduction to data analysis
- Unix environment for bioinformatic analysis
- Introduction to the Linux system
- Basic commands in Terminal and their practical use
- Overview of common data formats
Day 2-3: Basic operations with NGS data - Get a full picture of NGS workflow!
- Working with data from NCBI and other databases (SRAtool kit)
- Quality control of sequence data (FastQC, MultiQC, …)
- Editing sequences in various programs (FASTX-Toolkit, …)
- Introduction to alignment
- Read mapping (BWA, Bowtie2, …)
- Preparation of the reference sequence
- Alignment visualization (Tablet, IGV, UCSC, …)
Day 4: De novo assembly - Theory and hands on until you master...
- Different approaches to de novo assembly (Velvet, SPAdes, …)
- Evaluating assembly (Quast, …)
- Assembly visualization (Tablet, …)
Day 5: Variant Calling - Explore the open source world of variants!
- Preparation of sequencing data
- Identification of variants - SNPs, INDELs (SAMtools, GATK, …)
- SNP analysis
- Annotation of variants (SnpEff)
- Visualization of variants
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.
- Michal Kolář, Bioinformatician, Institute of Molecular Genetics
- Ondřej Lukšan, NGS Lab specialist
- Jan Pačes, Bioinformatician, Institute of Molecular Genetics
- Štěpán Stočes, Bioinformatician
- Petr Vácha, NGS Application specialist
- Language: English
- Registration fee includes: Workshop materials, Lunches/Coffee breaks
- Events: Vltava River Sightseeing Cruise + Conference dinner (both also 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.
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.