ONLINE COURSE – Genome Assembly and Annotation (GAAA01) This course will be delivered live

Genome assembly is the process of piecing together fragments of DNA to recontruct the original genome. The genome provides crucial information for understanding genetic structure, function and variation.

In recent years, long-read sequencing technologies have revolutionized genome assembly. These long reads can span repetitive sequences and structural variations making genome assembly simpler but also reducing gaps and fragments in the genome, resolve repeats, help with the detection of structural variation as well as improved haplotype phasing.

During this course we will look at data generated using PacBio and Oxford Nanopore, discuss the pros and cons of both sequencing technologies and the effect they might have on genome assembly. During the course we will look at different tools available to generate assemblies, focussing on de novo genome assembly. Polishing using short or long reads and the introduction of Hi-C sequencing can increase completeness of the genomes. At the difference steps during the assembly process we will look at the contiguity, completeness and correctness of the generated genomes, thereby evaluation the status of the genome.

Once a genome has been assembled the next step is annotation. Genome annotation involves identifying and mapping locations of genes and other functional elements within the sequenced genome. We will take a look at the differences between prokaryote and eukaryote genomes and the tools available for annotation. We will talk about steps to improve annotation once the automatic annotation has been made.

By the end of the course, participants should:

• Know the difference between Nanopore and PacBio data
• Be able to assembly genomes
• Be able to assess the generated genomes
• Assemble genomes integrating Hi-C data
• Know how to annotated a genome