Read alignment and small size variants calling (08/03/2017 - 09/03/2017)

The GenoToul bioinformatics platform, Sigenae, NED (GenPhySE) and TWB offers 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 software. This training session, organized jointly with the Sigenae platform, is designed to help you deal with NGS data, in particular Roche 454 and Illumina Solexa technologies with command line. You will discover the new sequence formats, the new 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 12:30 am): Variant calling. VCF format. Variant annotation (SNPeff / SNPsift).


The session will take place in the formation room of the INRA center of Toulouse-Auzeville.

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Prerequisites: ability to use a Unix environment (see Unix training). Training materials will be available on the website before the session. Slides in a “taking notes” format will be downloadable from our web site. A Unix reference command leaflet and a workbook will also be provided. Only the latter will be available during the session. Tool box: FastQC, BWA, Samtools, Picard tools, GATK, SnpSift / SnpEff, IGV.


  Current version of slides are available here.(Do not print this version before having the information that this slides are at the last version).


Bookings: Read alignment and small size variants calling
Ticket Type Price Spaces
for non-academic: 550€ + 20% taxes (TVA)
for INRA's staff: 165€ duty free per day for academic but non-INRA: 165€ + 20% taxes (TVA) per day