Genome assembly using long-reads
Genome assembly using long-reads
25 January 2027, 09h30-17h00
Optional Q&A session: 3 February 2027, 10h00-12h00 - online & room L4
General context
High-quality genome assemblies are essential for understanding the biology, evolution, and functional genomics of organisms. Advances in long-read sequencing technologies, such as Oxford Nanopore, now make it possible to generate highly accurate reference genomes, even for complex or repetitive regions.
This hands-on training introduces you to the principles and practical steps of genome assembly with long reads. You will learn how to design efficient sequencing strategies, process and assess raw reads, execute assembly workflows, and evaluate the quality of the final genome. By the end of the training, you will have the knowledge and skills to make informed decisions throughout an assembly project and prepare a robust foundation for downstream analyses.
- Describe the main steps of a genome assembly pipeline.
- Apply quality control procedures to filter and assess raw sequencing reads.
- Execute genome assembly using selected tools and adjust parameters.
- Evaluate the quality and completeness of a genome assembly.
- Reflect on potential next steps and downstream applications.
This training combines practical exercises with expert guidance. You will have the opportunity to work with the demonstrated tools and can choose to use your own datasets. An optional follow-up Q&A session is scheduled to address questions related to tools, parameter choices, and interpretation of results.
- Basic command-line skills (available via our Linux command line training)
- Experience with HPC/VSC environments (covered in our dedicated HPC training)
Tools and software
- pod5-file-format
- dorado
- BUSCO
- Porechop
- Miniasm
- hifiasm
- Flye
- QUAST/5.2.0-foss-2021a
- medaka
This course is part of the learning path Bulk long-reads for assembly or variants.
AI methods used
This course includes limited but important use of AI/ML: Dorado applies machine learning to convert raw nanopore signals into base calls, and Medaka uses neural-network models to improve consensus sequences during polishing.
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.
Practical info
25 January 2027
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
25 January 2027
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
25 January 2027
Ghent - VIB/UGent FSVM II
Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
Shared bicycles:
Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic
There are also some public bicycle pumps at the park.
25 January 2027
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.