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Terminal, Unix & Files

UZH BIO392 HS23 - Day 03

Izaskun Mallona (email: izaskun.mallona at

Morning (on site)

We will have two lectures and several sets of exercises (on site).

  • Unix + genomic formats lectures (exercises 1-4)
  • Unix and genomic formats exercises (5-14)


We will run the SIB Unix course using a Web browser. We encourage you to run the exercises of the course in a terminal of your own; either on a GNU/Linux or MacOS; or with a Web browser-based emulator of your choice, like cocalc.

  • SIB Unix course: UNIX for Bioinformatics
  • Chapter 1: What is UNIX
  • Chapter 2: The UNIX filesystem
  • Chapter 3: UNIX shell - first steps
  • Chapter 4: UNIX shell - filesystem commands
  • Chapter 5: UNIX shell - working with files


UNIX training


File formats


Exercises provide a flow of learning by doing.

  • Exercises. Exercises 5-14 cover FASTA and FASTQ.

You can launch a terminal in MacOS and GNU/Linux. If running another OS, plese make use a a Web-browser based emulator or a Linux virtual machine.


For extra/advanced reading, please check the following tutorials on bash and awk: