Usage of NGS is increasing in several biological fields due to a very rapid decrease in cost. However, it often results in hundreds of Gbs of data making the downstream analysis very challenging and requires bioinformatics skills.
In this module, we will introduce the most used sequencing technologies and explain their decryption concepts.
We will also introduce the repositories e.g. the European Nucleotide Archive (ENA), Sequence Read Archive (SRA) from which you could retrieve raw data based on specific experiments. We will practice the usage of command line tools to search and fetch NGS raw data in a powerful way.
Finally, using different datasets, we will practice screening for quality control, filtering reads for better downstream analysis, mapping reads to reference genome and visualize the output.