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.

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.

 - 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 – 1:00–7:00 PM (Berlin time)

• Why Unix?

• White spaces and case sensitivity

• 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

Tuesday – 1:00–7:00 PM (Berlin time)

• How do paths work? Absolute vs. relative paths

• Increasing productivity with tab completion, shortcuts, and wildcards

• Running programs in the background with Screen

• System management: monitoring power, memory, and disk space usage

• Installing software and managing environments with conda

Wednesday – 1:00–7:00 PM (Berlin time)

• Filesystem and permission system

• Users and groups

• Manipulating text files with Vim

• Turning data into information with filters

• Searching for files in the system

Thursday – 1:00–7:00 PM (Berlin time)

• Tabular data: definition and manipulation

• Processing large files with AWK

• Redirection and piping: communicating commands and files

• Introduction to shell scripting

Friday – 1:00–7:00 PM (Berlin time)

• Building a bioinformatics pipeline with shell

• Customization:

  • Environment variables

  • Custom prompts

  • Soft links

  • SSH configuration

• Final questions

• Bonus: some other useful commands