Short-read alignment and small size variants calling

Short-read alignment and small size variants calling (13/11/2023 - 14/11/2023)

The GenoToul bioinformatics platform, Sigenae and NED (GenPhySE) organize a series of training courses to familiarize yourself with the various resources it provides. These resources are currently: the hardware infrastructure, biological data banks and widely used bioinformatics softwares. This training session, organized jointly with the Sigenae platform, is designed to introduce NGS data, in particular Illumina Solexa technologies with command line. You will discover the new sequence formats, the assembly formats and the known biases of these technologies. You will use mapping on reference genome software, polymorphisms detection with the GATK pipeline and alignment visualization software.



This training is focused on the practice. It consists of modules with a large variety of exercises:

  • Day 1 (09:00 am to 12:30 am): Fastq format / Sequence quality. Read mapping.
  • Day 1 (14:00 pm to 17:00 pm): SAM format. Visualisation.
  • Day 2 (09:00 am to 17:00 am): Variant calling. VCF format. Variant annotation (SNPeff / SNPsift).


The session will take place in the room ‘salle de formation’ at INRAE center of Toulouse-Auzeville.


Prerequisites: ability to use a Unix environment (see Unix training) and Cluster (see Cluster training).


Training materials are available at :

– slides : training slides

– tutorial : tutorial for practical work


Bookings: Short-read alignment and small size variants calling

This event is fully booked.