Variant analysis using long-reads
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.
Learning outcomes
- 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.
Approach
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.
Required skills
- 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.
Extra information
This course is part of the learning path Bulk long-reads for assembly or variants