Introduction to Bioinformatics (M413)

Martin Reczko - Alexandros Dimopoulos



The course introduces students into the basic concepts of bioinformatics. It starts with a general overview of the various fields of bioinformatics and introduces dynamic programming as a solution to the sequence comparison problem (1). Next, a first introduction to the GNU / Linux operating system and the hands on use of basic command-line commands (CLI) as well as bash scripting is given. In addition, basic bioinformatics command line programs such as bedtools, vcftools, samtools, etc. are presented and used (2+3). Students are then familiarized with the programming language R, the use of IDE RStudio and the basic tools provided by the Bioconductor repository (4+5). Next, detailed examples of

NGS bioinformatics analysis and pipelines are explained for:

  • RNAseq (quality control, gene expression analysis) (6),
  • denovo assembly (both on the genome and transcriptome level) (7)
  • ChipSeq, ClipSeq and (8)
  • variant calling (exome sequencing example using GATK) (9)

Finally, the concept of flux