Variant analysis using long-reads
Variant analysis using long-reads
30 January 2026, 09h30-17h00
Optional Q&A session: 6 February 2026, 13h00-17h00
General context
Understanding genomic variation is essential for uncovering the genetic basis of disease, evolution, and phenotypic traits. While short-read sequencing has long been the standard, long-read technologies now offer superior resolution for detecting structural variants and phasing complex regions.
This course is designed for researchers working with genomic data who want to explore the potential of long-read sequencing in variant analysis. You will gain hands-on experience using the GenomeComb package (https://derijkp.github.io/genomecomb/) to process long-read (and short-read) data, perform variant and structural variant calling, and annotate results.
- Prepare long-read sequencing data by performing adapter clipping and aligning reads to a reference genome.
- Identify single-nucleotide variants and structural variants from aligned long-read data.
- Compare variant calling results across multiple samples and sequencing methods by generating and interpreting multisample files.
- Annotate detected variants with genomic location, predicted functional impact, and potential phenotypic associations.
- Filter variant datasets based on quality metrics and functional relevance to refine analysis results.
You have the opportunity to explore the tools using your own data. Questions that arise during this process (about the tools, the parameters, or the interpretation of the results) will be answered during the Q&A session.
- Use basic Linux commands for file handling and navigation in a terminal environment. If you are unfamiliar with Linux or have never used a command-line interface, we strongly recommend completing our Linux command line training beforehand.
- Run jobs on a High Performance Computing (HPC) system, preferably via the Flemish Supercomputer Centre (VSC). If you have no prior experience with HPC systems, we recommend completing our HPC training beforehand.
This course is part of the learning path Bulk long-reads for assembly or variants
Trainers
Peter De Rijk
Dr. Peter De Rijk is responsible for the analysis of the data generated by Nanopore sequencing. To this end he develops and upkeeps the analysis pipelines and he is involved in analysis consulting, implementation, benchmarking and troubleshooting.
Practical info
30 January 2026
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
30 January 2026
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
30 January 2026
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.
30 January 2026
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.