Workshop: Biology on the Command Line

June 22 to June 26

Learn the tools to analyze next generation sequence data online.

Dr Rafe Lyall (CPSBB, Bulgaria) and Prof Nicola Illing (UCT, South Africa) invited applications to attend two virtual workshops for students and experimental biologists who wish to develop their skills to analyze next generation sequencing data.

Workshop 1: Biology on the Command Line

  1. Who: Anyone interested in learning to use the Linux command line (no prior experience required)
  2. What: Become proficient at navigating and using common command line utilities to view or analyse files and data
  3. When: June 22 to June 26


The first stumbling block for many experimental biologists when faced with a bioinformatics project is the need to work on a command line terminal in a Linux/UNIX environment. This skill is a prerequisite for any scientist wishing to analyze their NGS datasets (and many others). The primary focus of this workshop was to build familiarity with working on the command line. The workshop was suitable for those with absolutely no experience with Linux/UNIX systems (covering the basics such as file system navigation and viewing and manipulating files) and progresses to more advanced topics (grep, sed and awk, package installation and scripting). These topics were covereing the context of the biological sciences and so were also included in an introduction to the analysis of file types one might commonly find when analyzing NGS data (e.g. FASTA/FASTQ/BED/GFF formats).

The workshop was ran remotely, online, over a 5-day period. Though there were topics and tasks each day set, attendees were able to sign in each day and work at their own pace to achieve the daily objectives. Slack was used as a communication channel for questions and discussion, which is encouraged. Access to a personal Linux system was not a prerequisite: the workshop computing environment was consist of a remotely hosted JupyterHub server deployed by However, good internet access was necessary.

The schedule was taken between 4-8hrs daily to complete, depending on the level of computational/biological skills of the delegate. Optional worksheets were made available each afternoon for delegates to consolidate what they have learnt in the morning. Workshop course notes and materials remained available after the workshop.

There was no charge for this workshop, which was a part of the training activities of project RESIST.

Sign up for Workshop: Biology on the Command Line here, by June 15, 2020

These workshops are supported by funding from project RESIST, as well the University of Cape Town.
Rafe Lyall, Center for Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
Nicola Illing, Department of Molecular and Cell Biology, University of Cape Town, South Africa