A tutorial on the Linux command line (CLI) and its use in bioinformatics.

Programme

• The first commands - Open a terminal and start trying the first commands (like pwd, cd, mkdir, man, wget) and familiarise with absolute and relative paths.
• Text files and the command line - Some more commands (like find), and a first look at text files and their manipulation (wc, head, tail, grep).
• Redirection - how to save the output from programs, and the difference between standard output and standard error.
• Pipes - combining multiple commands with UNIX pipes
• IGV: A quick overview - Using IGV to inspect common file formats
• SSH and remote servers - Working on a remote server from the command line or using VS Code
• Some file formats:
  • FASTA files - how sequences are stored in FASTA files
  • SAM files - the Sequence Alignment/Map format, and how to manipulate it with samtools
  • A list of common formats

See also:

• Miniconda and Mamba - Solving the dependency hell of bioinformatics software (and how to install Miniconda and Mamba to do this)
• Bash learning resources - Links to other resources to learn Bash
• A bonus track on word frequencies - Zipf distribution: a video worth watching and the invite to try analyzing texts to see if they follow Zipf’s law