NGS Data Analysis

Organizer:

Amin Ardeshirdavani, PhD

KU LEUVEN

Faculty of Engineering Science

Leuven, Belgium

  • Introduction to the command line and important commands
  • Introduction to NGS file formats and databases 
  • Important bioinformatics toolkits  

 

NGS data analysis 

  • Raw sequencing files
  • Preprocessing raw reads 
  • Read mapping 
  • Mapping output
  • Variant calling
  • Variant annotation 
  • Variant classification based on ACMG
  • Variant prioritization- Clinical Interpretation
  • Clinical Report


Practical information:

  • The workshop will be 3 full days from 9:00 to 18:00 with two pairs of shorts (30 min) and one long (60 min) breaks.
  • The Participant will receive a link to a warmup hand-on coding document with some elementary command-line tasks after registration.
  • To do the tasks we provide a pre-configured Virtual Machine which has all the necessary tools and files needed for the workshop. Therefore, attendees need to bring a laptop with at least 30Gb of free storage space and a minimum 8Gb of memory. 


Workshop made of 5 section:

 

Section 1: Introduction

 

  1. Short introduction 
  2. Basic Linux command
  3.  Overview of data file formats
  4. Tools and databases for NGS data analysis   

Section 2: Primary analysis

  1. Primary quality analysis
  2. Alignment
  3. Variant calling
  4. General data quality assesment    

Section 3: Secondary analysis 

  1. Variant annotation
  2. Variant classification
  3. Variant prioritization  

Section 4: Tertiary analysis 

  1. Interpretation
  2. Clinical report 

Section 5: Conclusion 

  1. Case studies

 




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