Reads alignment and small size variants calling with Galaxy

Reads alignment and small size variants calling with Galaxy (08/10/2018 - 09/10/2018)

This training session, organized jointly with the Sigenae platform, is designed to introduce NGS data, in particular Illumina technologies. 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), polymorphisms annotation and alignment visualization software.

This training focuses on practice. It consists of four modules with a large variety of exercises described hereunder:

• Galaxy initiation (First day : 09:00 am to 12:00 am)
• Cleaning and alignment (First day : 13:30 pm to 17:00 pm): Fastq format / Sequence quality; reads mapping
• Alignment’s result (Second day : 09:00 am to 12:00 am):  SAM format, Visualisation.
• The GATK package (Second day : 13:30 pm to 17:00 pm): Variant calling, VCF format, Variant annotation (SNPeff / SNPsift)

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

Prerequisites: None.

Training materials (exercises and corrections) will be given to you during the session.

Slides and exercises.

Bookings: Reads alignment and small size variants calling with Galaxy