Registration:

Please register here

Date: 10-12 February 2025

10am – 3pm each day (with 1hr for lunch)

Venue

Online

Places

20 for each workshop

You will be contacted by our finance team for full payment. Once payment is made, your place will be confirmed and full details sent by our training team.

Registration fee

£323 – University of Edinburgh 

£340 – Other University, or registered charity, staff/students

£355 – Industry staff

Information

Contact our training team

Overview

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 exciting new 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.

Who this course is for

Aside from a basic understanding of molecular biology, attendees must have a working knowledge of how to use the Linux BASH command line – our 1-day “Linux for bioinformatics” course is a suitable background.

Instructor

Urmi Trivedi – Bioinformatics Team Leader, Edinburgh Genomics

Heleen De Weerd – Bioinformatician/Analyst, Edinburgh Genomics

Kathryn Campbell – Genomics and Bioinformatics Training Coordinator, Edinburgh Genomics

Workshop format

The workshop consists of presentations and hands-on tutorials.

Topics covered

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