Introduction to Linux for Genomics

10-11 June 2024





Two half days: 1pm - 5pm each day.





You will be contacted by our finance team for full payment. Once payment is made, your place will be confirmed and full details sent by our training team.

Registration fee

£100/£105/£110 (University of Edinburgh/Other University/Industrial employees)


Contact our training team

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).


"I thought it would be painful but it was actually fun!! #linux course. Thanks Tim & Nathan" (November 2021)

"Having never used Linux before I came away with a working knowledge of the command-line and the confidence to use it." (May 2016)



Tim Booth 

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)