Data Carpentry (Genomics) Workshop Online

Moi University

Aug 14-17, 2023

9:00 am - 1:00 pm EAT

Instructors: Parcelli Jepchirchir, Collins Kigen, Dr. Rispah Torrorey

Helpers: Brenda Kamau, Fredrick Kebaso, Samuel Mwasya, Bonface Onyango

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: P.O Box 3900-30100,Eldoret. Get directions with OpenStreetMap or Google Maps.

When: Aug 14-17, 2023. Add to your Google Calendar.

Requirements: Participants must bring 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 committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

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.

Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


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

Pre-workshop Survey

Post-workshop Survey



Before starting Pre-workshop survey
9:00 Set-up
9:30 Data Tidiness
10:00 Planning for NGS Project
10:30 Examining Data on the NCBI SRA Database
11:00 am Introduction to the Commandline Navigating files and Directories
12:00 Finish

Day 2

9:00 Working with files and directories
10:00 Redirection
11:00 Writing scripts and Working with Data
12:00 Project Organization
12:30 Finish

Day 3

9:00 Data Wrangling & Processing
10:00 Assessing Read Quality
11:00 Trimming and Filtering
12:30 Finish

Day 4

9:00 Variant Calling
11:00 Automating Variant Calling
12:00 Wrap -up
End Post-workshop survey


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