4th Prague Autumn School - De-Novo Assembly and Variant Calling Data Analysis Workshop

After three successful years we are again inviting you to join our data analysis workshop which covers all basic steps of Next-Generation sequencing data analysis.

This five day computationally-intensive workshop focuses on quality control, sequence editing, read mapping and alignment. Additionally, this year we will pay a special attention to genome assembly and variant calling and annotation.

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 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…

 


 

Workshop agenda:

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

 


 

Speakers

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
      

 

Workshop Logistics

  • 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.

 

Resources

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.

 


 

Please note:

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.

Event Dates

8. - 12.10.2018
08:30 - 17:00

Free seats: 12

Prague, Czech Republic

Conference Centre, Institute of Molecular Genetics, Videnska 1083, 14220 Prague, Czech Republic

Language: English

5 day

1 150 EUR

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