Processing short reads
Processing short reads
General context
Understanding how to handle and interpret Next Generation Sequencing (NGS) data is essential for researchers working with high-throughput omics. This introductory course is designed for researchers who are new to NGS analysis. It provides the background knowledge required to successfully complete advanced NGS analysis training
The course goes through the analysis pipeline of NGS data, starting from FASTQ files with raw reads to BAM files with reads aligned to a reference. Participants will gain a practical understanding of how NGS data is generated, formatted, and processed, including hands-on experience with quality control and mapping workflows. The course also introduces key tools and platforms, such as Galaxy, to support reproducible and accessible analysis.
- Describe the basic principles of the AVITI and Illumina sequencing platforms and their role in NGS workflows.
- Identify common NGS file formats (e.g., FASTQ, BAM) and demonstrate basic file handling operations.
- Perform quality control checks on raw NGS data using standard tools and interpret the results.
- Execute a basic mapping workflow for NGS data and explain the purpose of each step.
- Navigate the Galaxy platform to run simple NGS analysis tasks in a reproducible environment.
This is an e-learning course that involves analyzing an example NGS data set.
None
- Galaxy: http://usegalaxy.be
- FastQC
- Trimmomatic
- Bowtie/BWA/minimap
- STAR/HISAT2
- Kallisto/Salmon
- Qualimap
- RSeQC
- IGV
This course is part of multiple learning paths.
Trainers
Janick Mathys
Janick tries to help VIB scientists analyze their data by offering bioinformatics training and support. Next to organizing trainings, creating e-learning courses and teaching statistics, R, Python, Linux, HPC, bulk and single cell RNA-Seq analysis, she consults scientists and develops pipelines for omics analyses. Before joining VIB, she worked as a post-doc at KULeuven, doing research on transcriptomics and transcription regulation. She coordinated the Master of Bioinformatics program of KULeuven and taught the course on Biological Databases.