High-Quality Genome Assembly with Long-Read Technology
18/04/2024
06/05/2024
General context
The plummeting costs for sequencing over the last decades, allow whole genome resources to be built in a single lab, for a single project. While accessible to most, the process still demands informed decision-making and navigation through potential pitfalls.
High-quality genome assemblies are key for deciphering the biology of an organism, paving the way for diverse downstream analyses:
- genetic variations: Identify mutations linked to disease, adaptation, or other phenotypes.
- gene function: Delve into the roles and networks of genes within the organism.
- evolutionary history: Chart the path of genetic divergence and understand relationships between species.
- comparative insights: Analyze similarities and differences across genomes to uncover broader biological principles.
Genome assembly has been revolutionized by long-read sequencing technologies, particularly by PacBio HiFi and Oxford Nanopore Technology. These technologies overcome the limitations of short-read methods, in assembling complex genomes with high levels of repetitive regions. As a result, they are currently the obvious choice for generating de novo reference genomes.
While a number of assembly pipelines and algorithms exist, informed decision-making, from defining your project goals and crafting optimal sequencing strategies to assessing the final assembly, each step holds critical implications for success.
Ultimately, the reward is a reference genome of your target organism that will lay the foundation on which downstream experiments can be built.
In this course we will:
- discuss some considerations prior to approach the sequencing of a genome
- go through an assembly pipeline
- teach you how to do proper quality control and filtering of reads, run assemblies while discussing parameters to consider and touch on “what next”
Participants should have some experience with Linux, and running jobs using the HPC/VSC. You should attend the Linux training to get acquainted with the environment. We organize a Linux session and an HPC session on Friday April 12th in Ghent. Please join the waiting list of these trainings if you want to attend them. Contact janick.mathys@vib.be if you want to follow the Linux/HPC introduction training but you cannot make it on April 12th.
Trainers
Stephane Rombauts
Stephane Rombouts is staff scientist in the Van de Peer Lab of the VIB Center for Plant Systems Biology, where he maintains the PlantCARE database of plant promoters and regulatory elements. He is also involved in the annotation of new plant genomes using the Eugene gene prediction platform that he collaborated on.
Heloise Bastiaanse
Heloise Bastiaanse is a post-doctoral researcher in the Bio-energy and Bio-aromatic group of Prof. Wout Boerjan in the VIB Center of Plant Systems Biology. She works on the project ‘POPMET’, aimed at the large-scale identification of metabolites, metabolic pathways and their genes in the model tree poplar using cutting-edge -omics technologies in 650 genotypes collected along the main rivers of Europe.
Practical info
18 April 2024 - 06 May 2024
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
18 April 2024 - 06 May 2024
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take bus 49, 50 or 70 to Technologiepark. Please check Routeplanner De Lijn for schedules.
18 April 2024 - 06 May 2024
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket and have it validated at the reception desk of the FSVM building. Parking will only be allowed in regular parking spots (for instance in front of the building) and in the new parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited and after initial warnings, fines will be issued (€ 50).
18 April 2024 - 06 May 2024
Ghent - VIB/UGent FSVM II
Room L4 of the FSVM2 building, Technologiepark, Gent