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).

Tool box: FastQC, BWA, Samtools, Picard tools, GATK, SnpSift / SnpEff, IGV.