This course is fully booked (no waiting list)

The course will start with an overview of current NGS technologies and directions in which these are currently progressing. Methods for assembling genomes from NGS data using either a reference genome or de novo assembly will be presented together with some emphasis on assessing NGS data quality (Quality control, accuracy of base calling). The course will then offer an overview of the range of biological/biomedical questions that these new types of data can help to address. This includes:

• The use of NGS resequencing of closely related genomes for detecting mutations. This includes the characterization of somatic mutations in cancer tissues, the de novo mutation spectrum in eukaryotic genomes, and the detection of mutations underlying phenotypic changes in experimental or natural populations.
• Combining NGS with methods aimed at reducing genome complexity such as exome resequencing in complex genomes.
• The use of resequencing of a large number of individuals for Single Nucleotide Polymorphism (SNPs) and Copy number variation detection.
• Application of NGS in Transcriptomics, Epigenomics and Chromatin structure studies. Environmental/Meta-genomics studies probing the bacterial/viral diversity of understudied biomes.
• Comparative and evolutionary genomics.

To allow hands-on data analysis training, the course includes the following computer exercises, which can be completed using either your own or example data:

• Introduction to Galaxy, GATK and Samtools.
• Grooming of reads.
• Mapping of Illumina reads to reference.
• SNP/indel calling, filtering and annotation.
• Gene models and transcript quantification.