Short programme

Example program of one day training. The actual timetable will be adjusted according to the trainees needs.

• Short tutorial

When	What
9.30 - 10.30	Introduction to the Linux Command Line Interface
	• General concepts
	• Working with remote servers
	• Filesystem and basic commands (ls, pwd, cd...)
	• Directories (mkdir, rmdir)
	• Using find to locate files
	• Anticipating more commands if time allows
	🔧 Practical: Logging in and looking around
10.30 - 10.45	Short Break
10.45 - 11.30	Text files and bioinformatics formats
	• What is a "simple text" file
	• Viewing a text file (cat, head, tail, less, wc)
	• FASTA format
	• FASTQ format
	• BED/GFF/GTF formats
	• SAM (BAM) format
	🔧 Practical: Extracting information from text files
11.30 - 11.45	Short Break
11.45 - 12.45	Bioinformatics from the command line
	• More commands (like grep, cut, sort...)
	• Program pipes and redirections
	• Using bioinformatics tools (like bwa and samtools)
	🔧 Practical: Program pipes and redirection