Data Carpentry (Genomics) Workshop - Online

National Institute for Theoretical and Computational Sciences (NiTheCs)

August 1-5, 2022

9:00-13:00 UTC+2 (South Africa)

Instructors: Mamana Mbiyavanga, (UCT), Nikki Gentle (WITS), Ryan Daniels (UWC)

Helpers: Parcelli Jepchirchir

General Information

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: August 1-5, 2022. Add to your Google Calendar.

Requirements: Participants must have a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email , , or for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Due to the online nature of this workshop, the programme allows for regular breaks on the hour. For example we will start at 09:00 then break at 9:50 to 10:00 and then continue for 50 minutes again till 13:00

Day 1

09:00 Pre-workshop survey & Introduction - Nikki Gentle
09:30 Project Organization and Management - Nikki Gentle
  • Setup
  • Data Tidiness
  • Planning for NGS Projects
  • Examining Data on the NCBI SRA Database
11:00 Introduction to Cloud Computing for Genomics - Nikki Gentle
  • Why of cloud computing
  • Logging onto Cloud
12:00 Finish

Day 2

09:00 Introduction to the Command Line - Mamana Mbiyavanga
  • Setup
  • Introducing the Shell
  • Navigating Files and Directories
  • Working with Files and Directories
  • Redirection
12:00 Finish

Day 3

09:00 Continuation: Introduction to the Command Line - Ryan Daniels
  • Writing Scripts and Working with Data
  • Project Organization
12:00 Finish

Day 4

09:00 Data Wrangling and Processing - Ryan Daniels
  • Setup
  • Background and Metadata
  • Assessing Read Quality
  • Trimming and Filtering
12:00 Finish

Day 5

9:00 Continuation: Data Wrangling and Processing - Mamana Mbiyavanga
  • Variant Calling Workflow
  • Automating a Variant Calling Workflow
11:30 Introduction to Cloud Computing for Genomics - Ryan Daniels
  • Fine tuning your Cloud Setup
  • Which Cloud for my data?
Post-workshop survey
12:00 END


To participate in a Data Carpentry workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The setup instructions for the Data Carpentry Genomics workshops can be found at the workshop overview site