Winter School in Bioinformatics
Dates: Online - January 16th-20th (2-8 pm Berlin time zone)
Overview
This course will introduce participants to the field of Next Generation Sequencing biology, understanding both the concepts and handling of the data. We will cover a broad range of software and analyses from quality assessment of sequencing runs, through assembling and annotating small genomes, RNAseq and differential gene expression, and phylogenomics with NGS data. Primarily focused on Illumina data, we will also look at the different requirements and opportunities when utilizing long-read data (Nanopore/PacBio). This course will be accompanied by sessions on the use of the Linux command line, and Docker which is the preferred platform for most bioinformatic analyses, as well as software containers, through Docker or Singularity, with a particular focus on best practices for reproducibility.
Learning outcomes
- Effectively handling NGS data comfortably and in a reliable and reproducible manner
- Understanding the strengths and pitfalls of NGS and how to assess the quality of data generation and analysis
- Hands-on experience with state-of-the-art methods to use NGS in experiments across a range of approaches (genomics, transcriptomics, phylogenomics)
- Assessment of strengths and weaknesses of the different DNA sequencing technologies, both short read (Illumina), and long reads (Pacific Bioscience, Oxford Nanopore).
- Familiarity with biological sequence analysis in an evolutionary context
