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Introduction to Linux for Genomics workshop, Jan 23 - 24

Genomic studies produce vast amounts of data, usually in the form of very large text files. Linux is particularly suited to working with such files, and is therefore arguably one of the most important tools in a bioinformatician’s toolkit. The Linux command-line enables one to view, filter and manipulate large text files that are difficult or impossible to handle with applications like Word or Excel, write pipelines to perform certain tasks, and run bioinformatics software for which no web interface is available. In this workshop we will first cover the most used Linux commands, followed by a short introduction to several popular command-line tools that were especially developed for genomics as well as file formats commonly used in genomics (BED, FASTA, FASTQ, GFF/GTF, SAM/BAM, VCF).


Tim Booth & Nathan Medd

Workshop format

The workshop consists of guided tutorials and hands-on exercises. Roughly 3/4 of the workshop will be spent on Linux and 1/4 on command-line tools for genomics and file formats.

Who should attend

Graduates, postgraduates, and PIs, without any previous command-line experience, who want to learn to use the Linux command-line in order to be able to work with large data files.


A general understanding of molecular biology and genomics, and elementary skills in computer usage are required.

A computer with stable internet connection and a VNC viewer (download instructions included)

Topics covered

  • The shell and commands
  • Getting help
  • Files and directories
  • Navigating the file system
  • File management
  • Permissions
  • Accessing files
  • Downloading remote files
  • Zipping and unzipping files
  • Pipes and redirects
  • Filtering / manipulating file content
  • Shell scripts
  • Process management
  • Command-line tools for genomics (seqtk, bioawk, samtools, bedtools, tabix)

Related Links

Edinburgh Genomics