Hands-On introduction to NGS variant analysis

Hands-On introduction to NGS variant analysis


Technologiepark, Ghent

Start date:

20 January 2020

20 January 2020

from 10h00 to 17h00

21 January 2020

from 10h00 to 17h00

General context

This training gives an introduction to the use of several popular NGS analysis software packages.


Using a full publicly available chromosome read-set from one of the 1000 genome samples:

  • ​Perform a complete analysis workflow including QC, read mapping, read coverage analysis, and variant calling against the human reference genome.
  • Use GenePattern and open source software to evaluate each step of a classical NGS variant workflow and feel the complexity of the task.
  • Quickly compare the obtained results with gold standard public data

The skills acquired during this session should allow participants understand what variant calling implies.

Participants with experience in command line can do the workflow using command line tools.

Required skills

Skills required to follow this training include basic knowledge of Illumina NGS read structure. People who lack knowledge of Illumina reads should follow the 'Introduction to the analysis of NGS data' training first.

Not in the scope
  • similar workflow(s) using commercial products like the 'CLC genomics workbench'
  • similar workflow(s) using the free Galaxy GUI (although perfectly doable using the acquired knowledge)
  • variant analysis at multi-genome level & GWAS (<- advanced computing and statistical expertise required).
  • structural variant analysis (large indels, translocations, CNV) as being too complex with no all-in-one tool available.


Stéphane Plaisance

Stéphane Plaisance is a bioinformatitician at the VIB Nucleomics Core in Leuven.

Contact Stéphane Plaisance :
Tuur Muyldermans

Tuur Muyldermans is a bioinformatics trainer at the VIB Bioinformatics Core and ELIXIR Belgium. 

Contact Tuur Muyldermans :


To be added

To be added

Practical info

Location & Venue

20 January 2020 - 21 January 2020


Technologiepark-Zwijnaarde 126
9052 Gent

Public transport

20 January 2020 - 21 January 2020

Public transport

Several buses drive between Gent Sint-Pieters railway station and Technologiepark: Bus 70, 71 and 72 (‘Tramstraat’)

  • Get off at the stop marked 'Bollebergen' at Grote Steenweg Noord.

  • Technologiepark is straight in front of you on the other side of the soft verge.

  • Walk into the park to the roundabout. You can see the iGent Tower on your left.

Shuttle bus

  • The shuttle service between Gent Sint-Pieters and Technologiepark runs every 15 minutes during peak hours (7.30 - 9.30 am and 4.30 - 6.30 pm).

  • The site has four stops, including one nearly in front of the iGent Tower (4th stop).

  • More info on the Tech Lane Ghent Science Park site.

Route description

20 January 2020 - 21 January 2020


You can park your car on the Tech Lane Ghent Science park in the open car parks (no barriers), like the one in front of the iGent tower across the road. These car parks have Dutch signs which read "Parkeren uitsluitend met vignet! (overtreding = wielklem)”. This means you should only park there if you have a valid car park permit. You can request such a permit by sending an email to your contact person at iGent. The permit is only valid for a single day, and will need to be placed visibly behind the car's windscreen.

Venue contact

20 January 2020 - 21 January 2020