Workshop: De-novo Assembly with a Special Focus on Virus Detection

18. - 22.11.2019 08:30 - 17:00 Brno, CZECH REPUBLIC 1 250 € without VAT English Seats available: 0

In Autumn 2019, we are launching a new data analysis workshop aiming at de-novo assembly with a particular focus on virus detection and identification.

Similarly as our other events, this five-day workshop includes a necessary speaker-supervised intro into NGS data analysis (day 1-3) which has been tailored to lead into the de-novo assembly session (day 4) whose results, obtained by using a small RNA data set, are run through a data analysis pipeline to detect viruses (day 5).

After successfully finishing the workshop participants will be able to perform virus discovery using deep sequencing of small RNAs by applying de novo assembly approach (keeping in mind it will all be demonstrated using small tailored data sets to make it doable in a time-limited session).

 

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, with a special focus on virus detection. No prior knowledge of sequences data analysis or specific programming skills are required.

 

What will you learn?

  • How to perform basic manipulation with raw sequences and read mapping
  • How to detect viruses by using de-novo assembly of raw reads 
  • 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 continue on when you return to your desk!


 

During the workshop…

  • Trainers will be delivering their lectures and guiding you through hands-on exercises
  • Every participant works independently using an assigned powerful computer - there are frequent hands-on sessions during the workshop to give you a chance to practice all steps of the workflow!
  • No personal laptops are required/allowed

 


 

Workshop agenda

Day 1 – Introduction to data analysis:

  • General introduction to NGS data analysis
  • Basic commands in Terminal and navigation
  • Overview of common bioinformatics file formats
  • NGS databases (UCSC, ENSEMBL, NCBI)
  • Unix commands for manipulation of NGS data
  • Combining commands by piping

Day 2 – Preprocessing NGS data:

  • The AWK language – text processing
  • Current sequencing technologies – basecalling specifications
  • Quality control of raw sequence data (FastQC, MultiQC)
  • Editing raw sequences
  • Introduction to alignment (Local vs Global)

Day 3 – Read mapping / Alignment:

  • Read mapping
  • microRNA alignment techniques
  • Mapping onto the host reference genome (BWA, Bowtie2)
  • Manipulation with mapping outputs (samtools, bamtools, bedtools)
  • Mapping statistics
  • Mapping validation

Day 4 – De novo Assembly:

  • Visualization of mapped reads (IGV, Tablet)
  • De-novo assembly using various algorithms (OLC vs DBG)
  • Transcriptome and RNA assembly
  • Genome and transcriptome structure
  • Evaluating assembly
  • Assembly visualization

Day 5 – Virus detection:

  • Manipulation with contig sequences
  • Basic Local Alignment Search Tool (Blastn, Blastx)
  • Virus detection using virus database
  • Small RNA size profiling
  • Summary

 


 

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.

  • Pavlína Kočová, Bioinformatician
  • Štěpán Stočes, Bioinformatician
  • Petr Vácha, NGS Application specialist
      

 

Workshop Logistics

  • Language: English
  • Registration fee includes: Workshop materials, Lunches/Coffee breaks
  • 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 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.


Workshop: De-novo Assembly with a Special Focus on Virus Detection

When: 18. - 22.11.2019
Time: 08:30 - 17:00
Where: Brno, CZECH REPUBLIC
Address: JIC INBIT, Kamenice 34, Brno
Price: 1 250 € without VAT
Language: English
Seats available: 0
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