Variant analysis using long-reads
Variant analysis using long-reads
27 January 2027, 09h30-17h00
Optional Q&A session: 3 February 2027, 10h00-12h00, room L4 & online
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
27 January 2027
Antwerp - Campus Drie Eiken UAntwerpen
Universiteitsplein 1
2610 Antwerpen
Belgium
27 January 2027
Antwerp - Campus Drie Eiken UAntwerpen
Antwerp has a dense public transportation network. Buses and trams are available to take you to many different parts of the city. There are direct bus links to various other towns and cities as well. Plan your route using the De Lijn timetables.
- Campus Middelheim - Campus Groenenborger: around 7 min. on foot
- Campus Middelheim - Campus Drie Eiken: around 35 min.
- Campus Groenenborger - Campus Drie Eiken: around 45 min.
- Stadscampus - Campus Middelheim: around 45 min.
- Stadscampus - Campus Groenenborger: around 55 min.
- Stadscampus - Campus Drie Eiken: around 60 min.
Did you know Antwerp also has a water bus? You can use it to travel between the Antwerp city centre and nearby towns.
27 January 2027
Antwerp - Campus Drie Eiken UAntwerpen
Antwerp is a bike-friendly city. Get to know the smart and cheap way to travel around in Antwerp fot students.
For short trips in and around the city, a rental bike is ideal. Apart from the student bicycle and the Velo city bikes, there are several other bike rental options.
Do you need to cross the Scheldt? Check the availability of the bike lifts and escalators of the tunnels, or take Antwerp’s ferry service with your bike.
Cycling between campuses:
- Stadscampus - Campus Middelheim: 20 min.
- Stadscampus - Campus Groenenborger: 25 min.
- Stadscampus - Campus Drie Eiken: 30 min.
- Campus Middelheim - Campus Groenenborger: 4 min.
- Campus Middelheim - Campus Drie Eiken: 10 min.
- Campus Groenenborger - Campus Drie Eiken: 8 min.
The newest way to travel around Antwerp is by shared electric scooter.
27 January 2027
Antwerp - Campus Drie Eiken UAntwerpen
It’s recommended to travel to and in Antwerp by public transport. If you are travelling by car, take the following into account:
- There are P+R zones where you can park on various main roads into Antwerp. They are ideal places to switch to bus, tram or bike a few kilometres from the campus.
- The Antwerp city centre and part of Linkeroever (Antwerp’s left bank) are a low-emission zone: highly polluting vehicles are not allowed into the city.
- Keep in mind that the zone around the Stadscampus is a residential area with a speed limit of 20 km/h. Pedestrians freely make use of the entire road.
- Take possible road works and events into account.
- Within Antwerp, you can make use of the taxi service.
Campus Drie Eiken en Campus Groenenborger have free university parking spots.
Carpooling is not only fun and ecological, but also good for your wallet and you get to meet new people. Are you looking for a car ride or a fellow passenger, occasionally or daily? Take a look at our carpool platform.