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) invite 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 will be to build familiarity with working on the command line. The workshop is 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 will be covered in the context of the biological sciences and so will also include 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 will be run remotely, online, over a 5-day period. Though there will be set topics and tasks each day, attendees will be able to sign in each day and work at their own pace to achieve the daily objectives. Slack will be used as a communication channel for questions and discussion, which is encouraged. Access to a personal Linux system is not a prerequisite: the workshop computing environment will consist of a remotely hosted JupyterHub server deployed by However, good internet access will be necessary.

We anticipate that the schedule will take between 4-8hrs daily to complete, depending on the level of computational/biological skills of the delegate. Optional worksheets will be made available each afternoon for delegates to consolidate what they have learnt in the morning. Workshop course notes and materials will remain available after the workshop has ended.

There is no charge for this workshop, which is being run as 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