Genome assembly using long-reads
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.
Learning outcomes
- 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.
Approach
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.
Required skills
- Basic command-line skills (available via our Linux command line training)
- Experience with HPC/VSC environments (covered in our dedicated HPC training)
Software demonstrated
Tools and software
- pod5-file-format
- dorado
- BUSCO
- Porechop
- Miniasm
- hifiasm
- Flye
- QUAST/5.2.0-foss-2021a
- medaka
Extra information
This course is part of the learning path Bulk long-reads for assembly or variants.