UNIX and shell scripting for bioinformatics


ONLINE, 16-20 January 2023

Due to the COVID-19 outbreak, this course will be held online



Advances in high-throughput biology have transformed modern biology into an incredibly data-rich science. Nowadays, biologists need to acquire basic computer programming in order to access and analyse their own data.
Many bioinformatic programs are developed to run in Unix or Unix-like operating systems, more specifically via the command line. In this course, students will be introduced to the most powerful Unix commands and they will learn how to connect to external resources/servers, install specialist tools and ultimately to combine commands into scripts for automation and reproducibility.
Hands-on sessions will focus on applying those tools to process biological data, explicitly next-generation sequencing (NGS) data.

Target audience

This course assumes no prior knowledge of Unix and shell scripting. Since most examples will be focused on biological data, some background in biology is desired.

Learning outcomes

- Mastering most popular Unix commands

- Creating and editing files using the command line

- Processing large files using Unix and bash scripting

- Automating bioinformatics pipelines by writing shell scripts 

- Managing system tasks and resources usage




Monday – Classes from 1 to 7 pm (Berlin time)


  - Why Unix?
  - White spaces and case sensitiveness
  - Introduction to linux commands
  - Using a Linux server - connecting and transferring files
  - Running the most popular commands
  - Manual pages: getting the most out of commands


COst overview

Package 1

480 €