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Training & Workshops

Introduction to Bash: Using the Terminal For Bioinformatics

This course is targeted at all researchers in biological and medical research wishing to develop their bioinformatics capacity, and is now offered over 4 x 2hr sessions across multiple days weeks. Sessions will be offered only on the North Terrace Campus and AHMS for Semester 2

Postgraduate students can receive credit for 8 CaRST hours upon completion of the course. Undergraduate Students and other researchers are also welcome.


This workshop is designed to give you the prerequisite skills for accessing High Performance Computing (HPC) machines, like Phoenix. Basic data management strategies will also be covered in the context of next generation sequencing data.

The specific areas which will be covered are:

  • Navigating through files and directories
  • Basic bash tools and commands
  • Regular Expressions
  • stdout, stderror and re-direction of output
  • The stream editor sed
  • Writing bash scripts
  • Basic job submission to a High Performance Computing (HPC) system

Course Dates

North Terrace Campus

The Braggs, Room 450

Wednesday 19th and 26th September, 2018

Session Date Time Topics Covered
Session 1 Wed 19th September 10:30am - 12:30pm
  • Navigating directories using bash
Session 2 Wed 19th September 1:30pm - 3:30pm
  • Working with files
Session 3 Wed 26th September 10:30am - 12:30pm
  • Regular Expressions 
  • The stream editor sed
Session 4 Wed 26th September 1:30pm - 3:30pm
  • Basic Scripting Techniques

Prerequisites and Co-requisite Courses

No prior experience is required, however all attendees are required to provide their own laptop. No specific OS is required.

This course serves as a prerequisite for Introduction to Next Generation Sequencing (NGS) Data


Course positions are strictly limited. To register for these sessions, please email a brief description of why you’d like to attend to

Introduction to NGS Data and Related Files


This is a full day workshop introducing you to the basic layout of important files used in high-throughput sequencing applications, such as fastq, bam, bed, vcf and gff files. In addition we will cover the key areas such as:

  • Assessing the Quality of your data
  • Aligning Reads to a Genome
  • Inspecting Files using Bash
  • Visualising Data
  • Identifying Variants

Postgraduate Students will be accredited for 6 CaRST hours.


Attendance at Introduction to Bash, or alternatively prior experience with Bash or an HPC environment

Course Dates

The Braggs, 450

Thursday Sept 27th



Registrations can be made here

Bioinformatics Hub

Level 4,
Santos Petroleum Engineering Building,
North Terrace Campus
The University of Adelaide
SA 5005


T: +61 8 8313 1207