Next-generation sequencing for beginners: applications to population genetics, forest health and tree breeding

Contact santiago.c.gonzalez.martinez@gmail.com

This summer school course was intended to give a brief introduction to new sequencing technologies (the so-called Next-Generation Sequencing or NGS) and their applications in forest research.

The first part of the course provided a general overview on the steps followed by a typical NGS project, covering the following topics:

• FASTQ format and sequence quality (Phred score and fastqc software)
• A simple pipeline: BWA + Samtools
• Visualization: IGV
• Identifying SNPs: Samtools
• Annotating SNPs: ensembl vep.pl
• Identifying structural variants
• RNAseq: tophat + cufflinks
• De novo assembly: SGA

The second part of the course focussed on applications of NGS to taxonomy, population genetics and breeding, including talks on adaptation to environmental changes, genomic selection and analysis of environmental samples. A hands-on workshop on genome-wide genetic association (GWAS) took place in the afternoon of the second day.